Protein production and protein delivery

ABSTRACT

The present invention relates to DNA constructs that alter the expression of a targeted gene in a cell when the DNA construct is homologously recombined with a target site within the chromosomal DNA of the cell, as well as to a cell into which has been incorporated a new transcription unit containing an exogenous regulatory sequence operatively linked to an endogenous gene of the cell&#39;s chromosomal DNA. These constructs and cells can be used in a method of altering expression of the targeted gene.

RELATED APPLICATION

This application is a continuation of application Ser. No. 08/451,894,filed May 26, 1995, issued as U.S. Pat. No. 5,968,502, which is adivisional of application Ser. No. 07/985,586, filed Dec. 3, 1992,abandoned, which is a Continuation-In-Part of application Ser. No.07/789,188, filed on Nov. 5, 1991, abandoned, and is also aContinuation-In-Part of application Ser. No. 07/911,533, filed on Jul.10, 1992, abandoned, and is also a Continuation-In-Part of applicationSer. No. 07/787,840, filed on Nov. 5, 1991, abandoned, all of which areincorporated herein by reference.

BACKGROUND OF THE INVENTION

Current approaches to treating disease by administering therapeuticproteins include in vitro production of therapeutic proteins forconventional pharmaceutical delivery (e.g. intravenous, subcutaneous, orintramuscular injection) and, more recently, gene therapy.

Proteins of therapeutic interest are generally produced by introducingexogenous DNA encoding the protein of therapeutic interest intoappropriate cells. Presently-available approaches to gene therapy makeuse of infectious vectors, such as retroviral vectors, which include thegenetic material to be expressed. Such approaches have limitations, suchas the potential of generating replication-competent virus during vectorproduction; recombination between the therapeutic virus and endogenousretroviral genomes, potentially generating infectious agents with novelcell specificities, host ranges, or increased virulence andcytotoxicity; independent integration into large numbers of cells,increasing the risk of a tumorigenic insertional event; limited cloningcapacity in the retrovirus (which restricts therapeutic applicability)and short-lived in vivo expression of the product of interest. A betterapproach to providing gene products, particularly one which avoids therisks associated with presently available methods and provides long-termtreatment, would be valuable.

SUMMARY OF THE INVENTION

The present invention relates to improved methods for both the in vitroproduction of therapeutic proteins and for the production and deliveryof therapeutic proteins by gene therapy. The present method describes anapproach which activates expression of endogenous cellular genes, andfurther allows amplification of the activated endogenous cellular genes,which does not require in vitro manipulation and transfection ofexogenous DNA encoding proteins of therapeutic interest.

The present invention relates to transfected cells, both transfectedprimary or secondary cells (i.e., non-immortalized cells) andtransfected immortalized cells, useful for producing proteins,particularly therapeutic proteins, methods of making such cells, methodsof using the cells for in vitro protein production and methods of genetherapy. Cells of the present invention are of vertebrate origin,particularly of mammalian origin and even more particularly of humanorigin. Cells produced by the method of the present invention containexogenous DNA which encodes a therapeutic product, exogenous DNA whichis itself a therapeutic product and/or exogenous DNA which causes thetransfected cells to express a gene at a higher level or with a patternof regulation or induction that is different than occurs in thecorresponding nontransfected cell.

The present invention also relates to methods by which primary,secondary, and immortalized cells are transfected to include exogenousgenetic material, methods of producing clonal cell strains orheterogenous cell strains, and methods of immunizing animals, orproducing antibodies in immunized animals, using the transfectedprimary, secondary, or immortalized cells.

The present invention relates particularly to a method of gene targetingor homologous recombination in cells of vertebrate, particularlymammalian, origin. That is, it relates to a method of introducing DNAinto primary, secondary, or immortalized cells of vertebrate originthrough homologous recombination, such that the DNA is introduced intogenomic DNA of the primary, secondary, or immortalized cells at apreselected site. The targeting sequences used are determined by(selected with reference to) the site into which the exogenous DNA is tobe inserted. The present invention further relates to homologouslyrecombinant primary, secondary, or immortalized cells, referred to ashomologously recombinant (HR) primary, secondary or immortalized cells,produced by the present method and to uses of the HR primary, secondary,or immortalized cells.

The present invention also relates to a method of activating (i.e.,turning on) a gene present in primary, secondary, or immortalized cellsof vertebrate origin, which is normally not expressed in the cells or isnot expressed at physiologically significant levels in the cells asobtained. According to the present method, homologous recombination isused to replace or disable the regulatory region normally associatedwith the gene in cells as obtained with a regulatory sequence whichcauses the gene to be expressed at levels higher than evident in thecorresponding nontransfected cell, or to display a pattern of regulationor induction that is different than evident in the correspondingnontransfected cell. The present invention, therefore, relates to amethod of making proteins by turning on or activating an endogenous genewhich encodes the desired product in transfected primary, secondary, orimmortalized cells.

In one embodiment, the activated gene can be further amplified by theinclusion of a selectable marker gene which has the property that cellscontaining amplified copies of the selectable marker gene can beselected for by culturing the cells in the presence of the appropriateselectable agent. The activated endogenous gene which is near or linkedto the amplified selectable marker gene will also be amplified in cellscontaining the amplified selectable marker gene. Cells containing manycopies of the activated endogenous gene are useful for in vitro proteinproduction and gene therapy.

Gene targeting and amplification as disclosed in the present inventionare particularly useful for turning on the expression of genes whichform transcription units which are sufficiently large that they aredifficult to isolate and express, or for turning on genes for which theentire protein coding region is unavailable or has not been cloned. Thepresent invention also describes a method by which homologousrecombination is used to convert a gene into a cDNA copy, devoid ofintrons, for transfer into yeast or bacteria for in vitro proteinproduction.

Transfected cells of the present invention are useful in a number ofapplications in humans and animals. In one embodiment, the cells can beimplanted into a human or an animal for protein delivery in the human oranimal. For example, human growth hormone (hGH), human EPO (hEPO), humaninsulinotropin and other proteins can be delivered systemically orlocally in humans for therapeutic benefits. Barrier devices, whichcontain transfected cells which express a therapeutic product andthrough which the therapeutic product is freely permeable, can be usedto retain cells in a fixed position in vivo or to protect and isolatethe cells from the host's immune system. Barrier devices areparticularly useful and allow transfected immortalized cells,transfected cells from another species (transfected xenogeneic cells),or cells from a nonhistocompatibility-matched donor (transfectedallogeneic cells) to be implanted for treatment of human or animalconditions or for agricultural uses (e.g., meat and dairy production).Barrier devices also allow convenient short-term (i.e., transient)therapy by providing ready access to the cells for removal when thetreatment regimen is to be halted for any reason. Transfected xenogeneicand allogeneic cells may be used for short-term gene therapy, such thatthe gene product produced by the cells will be delivered in vivo untilthe cells are rejected by the host's immune system.

Transfected cells of the present invention are also useful for elicitingantibody production or for immunizing humans and animals againstpathogenic agents. Implanted transfected cells can be used to deliverimmunizing antigens that result in stimulation of the host's cellularand humoral immune responses. These immune responses can be designed forprotection of the host from future infectious agents (i.e., forvaccination), to stimulate and augment the disease-fighting capabilitiesdirected against an ongoing infection, or to produce antibodies directedagainst the antigen produced in vivo by the transfected cells that canbe useful for therapeutic or diagnostic purposes. Removable barrierdevices can be used to allow a simple means of terminating exposure tothe antigen. Alternatively, the use of cells that will ultimately berejected (xenogeneic or allogeneic transfected cells) can be used tolimit exposure to the antigen, since antigen production will cease whenthe cells have been rejected.

The methods of the present invention can be used to produce primary,secondary, or immortalized cells producing a wide variety oftherapeutically useful products, including (but not limited to):hormones, cytokines, antigens, antibodies, enzymes, clotting factors,transport proteins, receptors, regulatory proteins, structural proteins,transcription factors, or anti-sense RNA. Additionally, the methods ofthe present invention can be used to produce cells which producenon-naturally occurring ribozymes, proteins, or nucleic acids which areuseful for in vitro production of a therapeutic product or for genetherapy.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic representation of plasmid pXGH5, which includesthe human growth hormone (hGH) gene under the control of the mousemetallothionein promoter.

FIG. 2 is a schematic representation of plasmid pcDNEO, which includesthe neo coding region (BamHI-BglII fragment) from plasmid pSV2neoinserted into the BamHI site of plasmid pcD; the Amp-R and pBR3220risequences from pBR322; and the polyA, 16S splice junctions and earlypromoter regions from SV40.

FIG. 3 is a schematic representation of plasmid pXEP01. The solid blackarc represents the pUC12 backbone and the arrow denotes the direction oftranscription of the ampicillin resistance gene. The stippled arcrepresents the mouse metallothionein promoter (pmMT1). The unfilled arcinterrupted by black boxes represents the human erythropoietin EPO gene(the black boxes denote exons and the arrow indicates the direction hEPOtranscription). The relative positions of restriction endonucleaserecognition sites are indicated.

FIG. 4 is a schematic representation of plasmid PE3neoEPO. The positionsof the human erythropoietin gene and the neo and amp resistance genesare indicated. Arrows indicate the directions of transcription of thevarious genes. pmMT1 denotes the mouse metallothionein promoter (drivinghEPO expression) and pTK denotes the Herpes Simplex Virus thymidinekinase promoter (driving neo expression). The dotted regions of the mapmark the positions of human HPRT sequences. The relative positions ofrestriction endonuclease recognition sites are indicated.

FIG. 5 is a schematic diagram of a strategy for transcriptionallyactivating the hEPO gene; the thin lines represent hEPO sequences; thicklines, mouse metallothionein I promoter; stippled box, 5′ untranslatedregion of hGH; solid box, hGH exon 1; open boxes, hEPO coding sequences;HIII, HindIII site.

FIG. 6 is a schematic diagram of a strategy for transcriptionallyactivating the hEPO gene; the thin lines represent hEPO sequences; thicklines, mouse metallothionein I promoter; stippled box, 5′ untranslatedregion of hGH; solid box, hGH exon 1; striped box, 10 bp linker fromhEPO intron 1; cross-hatched box, 5′ untranslated region of hEPO; andopen boxes, hEPO coding sequences; HIII, HindIII site.

DETAILED DESCRIPTION OF THE INVENTION Overview of the Invention

The present invention and the methods described in the applicationsincorporated herein by reference relate to transfected primary,secondary, and immortalized cells of vertebrate origin, particularlymammalian origin, transfected with exogenous genetic material (DNA orRNA) which encodes a clinically useful product, methods by whichprimary, secondary, and immortalized cells are transfected to includeexogenous genetic material, methods of producing clonal cell strains orheterogenous cell strains which express exogenous genetic material, amethod of providing clinically useful products in physiologically usefulquantities to an individual in need thereof through the use oftransfected cells of the present invention, methods of vaccinatinganimals for protection against pathogenic viruses or microbial agentsexpressing epitopes antigenically related to products expressed by thetransfected cells and methods of producing antibodies directed against aproduct made by the transfected primary, secondary, or immortalizedcells. Clinically useful products can be produced in vitro, bypurification from the transfected cells, or produced in vivo, byimplantation into a non-human animal or human (i.e., gene therapy).Whether produced in vitro or in vivo, the clinically useful products caninclude hormones, cytokines, antigens, antibodies, enzymes, clottingfactors, transport proteins, receptors, regulatory proteins, structuralproteins, transcription factors, anti-sense RNA. Additionally, themethods of the present invention can be used to produce cells whichproduce non-naturally occurring ribozymes, proteins, or nucleic acids.

In one embodiment, the present invention relates to a method of gene orDNA targeting in cells of vertebrate, particularly mammalian, origin.That is, it relates to a method of introducing DNA into primary,secondary, or immortalized cells of vertebrate origin through homologousrecombination or targeting of the DNA, which is introduced into genomicDNA of the primary, secondary, or immortalized cells at a preselectedsite. The targeting sequences used are determined by (selected withreference to) the site into which the exogenous DNA is to be inserted.The present invention further relates to homologously recombinantprimary, secondary or immortalized cells, referred to as homologouslyrecombinant (HR) primary, secondary or immortalized cells, produced bythe present method and to uses of the HR primary, secondary, orimmortalized cells.

The present invention also relates to a method of activating a genewhich is present in primary cells, secondary cells or immortalized cellsof vertebrate origin, but is normally not expressed in the cells or isnot expressed at significant levels in the cells. Homologousrecombination or targeting is used to replace or disable the regulatoryregion normally associated with the gene with a regulatory sequencewhich causes the gene to be expressed at levels higher than evident inthe corresponding nontransfected cell, or causes the gene to display apattern of regulation or induction that is different than evident in thecorresponding nontransfected cell. The present invention, therefore,relates to a method of making proteins by activating an endogenous genewhich encodes the desired product in transfected primary, secondary orimmortalized cells.

Several embodiments in which exogenous DNA undergoes homologousrecombination with genomic DNA of transfected (recipient) cells can bepracticed according to the present invention. In one embodiment,introduction of the exogenous DNA results in the activation of a genethat is normally not expressed or expressed in levels too low to beuseful for in vitro protein production or gene therapy. In a secondembodiment, sequences encoding a product of therapeutic utility aredirected to integrate into the recipient cell genome via homologousrecombination at a preselected site in the recipient cell's genome, suchthat the site of integration is precisely known and the site can bechosen for its favorable properties (e.g., the site allows for highlevels of expression of exogenous DNA).

In a third embodiment, the present invention describes a method ofactivating (i.e. turning on) and amplifying an endogenous gene encodinga desired product in a transfected, primary, secondary, or immortalizedcell. That is, it relates to a method of introducing, by homologousrecombination with genomic DNA, DNA sequences which are not normallyfunctionally linked to the endogenous gene and (1) which, when insertedinto the host genome at or near the endogenous gene, serve to alter(e.g., activate) the expression of the endogenous gene, and further (2)allow for selection of cells in which the activated endogenous gene isamplified. Amplifiable DNA sequences useful in the present inventioninclude, but are not limited to, sequences which encode the selectablemarkers dihydrofolate reductase, adenosine deaminase, and the CAD gene(encoding the trifunctional protein carbamyl phosphate synthase,aspartate transcarbamylase, and dihydro-orotase). Improved versions ofthese sequences and other amplifiable sequences can also be used.According to the present method, the amplifiable DNA sequences encodinga selectable marker and the DNA sequences which alter the regulation ofexpression of the endogenous gene are introduced into the primary,secondary, or immortalized cell in association with DNA sequenceshomologous to genomic DNA sequences at a preselected site in the cell'sgenome. This site will generally be within or upstream of a geneencoding a therapeutic product or at a site that affects the desiredgene's function. The DNA sequences which alter the expression of theendogenous gene, the amplifiable sequences which encode a selectablemarker, and the sequences which are homologous to a preselected site ingenomic DNA can be introduced into the primary, secondary, orimmortalized cell as a single DNA construct, or as separate DNAsequences which become physically linked in the genome of a transfectedcell. Further, the DNA can be introduced as linear, double stranded DNA,with or without single stranded regions at one or both ends, or the DNAcan be introduced as circular DNA. After the exogenous DNA is introducedinto the cell, the cell is maintained under conditions appropriate forhomologous recombination to occur between the genomic DNA and a portionof the introduced DNA. Homologous recombination between the genomic DNAand the introduced DNA results in a homologously recombinant primary,secondary, or immortalized cell in which sequences which alter theexpression of an endogenous gene, and the amplifiable sequences encodinga selectable marker, are operatively linked to an endogenous geneencoding a therapeutic product. Culturing the resulting homologouslyrecombinant cell under conditions which select for amplification of theamplifiable DNA encoding a selectable marker results in a cellcontaining an amplified selectable marker and a coamplified endogenousgene whose expression has been altered. Cells produced by this methodcan be cultured under conditions suitable for the expression of thetherapeutic protein, thereby producing the therapeutic protein in vitro,or the cells can be used for in vivo delivery of a therapeutic protein(i.e., gene therapy).

Additional embodiments are possible. The targeting event can be a simpleinsertion of a regulatory sequence, placing the endogenous gene underthe control of the new regulatory sequence (for example, by insertion ofeither a promoter or an enhancer, or both, upstream of an endogenousgene). The targeting event can be a simple deletion of a regulatoryelement, such as the deletion of a tissue-specific negative regulatoryelement. The targeting event can replace an existing element; forexample, a tissue-specific enhancer can be replaced by an enhancer thathas broader or different cell-type specificity than thenaturally-occurring elements, or displays a pattern of regulation orinduction that is different from the corresponding nontransfected cell.In this embodiment the naturally occurring sequences are deleted and newsequences are added. In all cases, the identification of the targetingevent can be facilitated by the use of one or more selectable markergenes that are physically associated with the targeting DNA, allowingfor the selection of cells in which the exogenous DNA has integratedinto the host cell genome. The identification of the targeting event canalso be facilitated by the use of one or more marker genes exhibitingthe property of negative selection, such that the negatively selectablemarker is linked to the exogenous DNA, but configured such that thenegatively selectable marker flanks the targeting sequence, and suchthat a correct homologous recombination event with sequences in the hostcell genome does not result in the stable integration of the negativelyselectable marker. Markers useful for this purpose include the HerpesSimplex Virus thymidine kinase (TK) gene or the bacterialxanthine-guanine phosphoribosyl-transferase (gpt) gene.

The present invention also relates to a method by which homologousrecombination is used to convert a gene into a cDNA copy (a gene copydevoid of introns). The cDNA copy can be transferred into yeast orbacteria for in vitro protein production, or the cDNA copy can beinserted into a mammalian cell for protein production. If the cDNA is tobe transferred to microbial cells, two DNA constructs containingtargeting sequences are introduced by homologous recombination, oneconstruct upstream of and one construct downstream of a human geneencoding a therapeutic protein. The sequences introduced upstreaminclude DNA sequences homologous to genomic DNA sequences at or upstreamof the DNA encoding the first amino acid of a mature, processedtherapeutic protein; a retroviral LTR; sequences encoding a marker forselection in microbial cells; a regulatory element that functions inmicrobial cells; and DNA encoding a leader peptide that promotessecretion from microbial cells. The sequences introduced upstream areintroduced near to and upstream of genomic DNA encoding the first aminoacid of a mature, processed therapeutic protein. The sequencesintroduced downstream include DNA sequences homologous to genomic DNAsequences at or downstream of the DNA encoding the last amino acid of amature, processed protein; a microbial transcriptional terminationsequence; sequences capable of directing DNA replication in microbialcells; and a retroviral LTR. The sequences introduced downstream areintroduced adjacent to and downstream of the DNA encoding the stop codonof the mature, processed therapeutic protein. After introducing into thecells each of the two DNA constructs, the cells are maintained underconditions appropriate for homologous recombination between theintroduced DNA and genomic DNA, thereby producing homologouslyrecombinant cells. Optionally, one or both of the DNA constructs canencode one or more markers for either positive or negative selection ofcells containing the DNA construct, and a selection step can be added tothe method after one or both of the DNA constructs have been introducedinto the cells. Alternatively, the sequences encoding the marker forselection in microbial cells and the sequences capable of directing DNAreplication in microbial cells can both be present in either theupstream or the downstream targeting construct, or the marker forselection in microbial cells can be present in the downstream targetingconstruct and the sequences capable of directing DNA replication inmicrobial cells can be present in the upstream targeting construct. Thehomologously recombinant cells are then cultured under conditionsappropriate for LTR directed transcription, processing and reversetranscription of the RNA product of the gene encoding the therapeuticprotein. The product of reverse transcription is a DNA constructcomprising an intronless DNA copy encoding the therapeutic protein,operatively linked to DNA sequences comprising the two exogenous DNAconstructs described above. The intronless DNA construct produced by thepresent method is then introduced into a microbial cell. The microbialcell is then cultured under conditions appropriate for expression andsecretion of the therapeutic protein.

Transfected Cells

As used herein, the term primary cell includes cells present in asuspension of cells isolated from a vertebrate tissue source (prior totheir being plated, i.e., attached to a tissue culture substrate such asa dish or flask), cells present in an explant derived from tissue, bothof the previous types of cells plated for the first time, and cellsuspensions derived from these plated cells. The term secondary cell orcell strain refers to cells at all subsequent steps in culturing. Thatis, the first time a plated primary cell is removed from the culturesubstrate and replated (passaged), it is referred to herein as asecondary cell, as are all cells in subsequent passages. Secondary cellsare cell strains which consist of secondary cells which have beenpassaged one or more times. A cell strain consists of secondary cellsthat: 1) have been passaged one or more times; 2) exhibit a finitenumber of mean population doublings in culture; 3) exhibit theproperties of contact-inhibited, anchorage dependent growth(anchorage-dependence does not apply to cells that are propagated insuspension culture); and 4) are not immortalized.

Cells transfected by the subject method fall into four types orcategories: 1) cells which do not, as obtained, make or contain thetherapeutic product, 2) cells which make or contain the therapeuticproduct but in smaller quantities than normal (in quantities less thanthe physiologically normal lower level) or in defective form, 3) cellswhich make the therapeutic product at physiologically normal levels, butare to be augmented or enhanced in their content or production, and 4)cells in which it is desirable to change the pattern of regulation orinduction of a gene encoding a therapeutic product.

Primary and secondary cells to be transfected by the present method canbe obtained from a variety of tissues and include all cell types whichcan be maintained in culture. For example, primary and secondary cellswhich can be transfected by the present method include fibroblasts,keratinocytes, epithelial cells (e.g., mammary epithelial cells,intestinal epithelial cells), endothelial cells, glial cells, neuralcells, formed elements of the blood (e.g., lymphocytes, bone marrowcells), muscle cells and precursors of these somatic cell types. Primarycells are preferably obtained from the individual to whom thetransfected primary or secondary cells are administered. However,primary cells can be obtained from a donor (other than the recipient) ofthe same species or another species (e.g., mouse, rat, rabbit, cat, dog,pig, cow, bird, sheep, goat, horse).

Transfected primary and secondary cells have been produced, with orwithout phenotypic selection, as described in the copending U.S. patentapplications Ser. Nos. 07/787,840 and 07/911,533 and shown to expressexogenous DNA encoding a therapeutic product including, for example,hGH, EPO and insulinotropin.

Immortalized cells can also be transfected by the present method andused for either protein production or gene therapy. Examples ofimmortalized human cell lines useful for protein production or genetherapy by the present method include, but are not limited to, HT1080,HeLa, MCF-7 breast cancer cells, K-562 leukemia cells, KB carcinomacells and 2780AD ovarian carcinoma cells. Immortalized cells from otherspecies (e.g., chinese hamster ovary (CHO) cells or mouse L cells) canbe used for in vitro protein production or gene therapy. In addition,primary or secondary human cells, as well as primary or secondary cellsfrom other species which display the properties of gene amplification invitro can be used for in vitro protein production or gene therapy.

Exogenous DNA

Exogenous DNA incorporated into primary, secondary or immortalized cellsby the present method is: 1) DNA which encodes a translation ortranscription product whose expression in cells is desired, or a portionof a translation or transcription product, such as a protein product orRNA product useful to treat an existing condition or prevent it fromoccurring (eg., hGH, EPO or insulino-tropin); or 2) DNA which does notencode a gene product but is itself useful, such as a transcriptionalregulatory sequence or DNA useful to treat an existing condition orprevent it from occurring.

DNA transfected into primary, secondary or immortalized cells can encodean entire desired product, or can encode, for example, the active orfunctional portion(s) of the product. The product can be, for example, ahormone, a cytokine, an antigen, an antibody, an enzyme, a clottingfactor, a transport protein, a receptor, a regulatory protein, astructural protein, a transcription factor, an anti-sense RNA, or aribozyme. Additionally, the product can be a protein or a nucleic acidwhich does not occur in nature (i.e., a novel protein or novel nucleicacid). The DNA can be obtained from a source in which it occurs innature or can be produced, using genetic engineering techniques orsynthetic processes. The DNA can encode one or more therapeuticproducts. After transfection, the exogenous DNA is stably incorporatedinto the recipient cell's genome (along with any additional sequencespresent in the DNA construct used), from which it is expressed orotherwise functions. Alternatively, the exogenous DNA can be used totarget to DNA that exists episomally within cells.

DNA encoding the desired product can be introduced into cells under thecontrol of an inducible promoter, with the result that cells as producedor as introduced into an individual do not express the product but canbe induced to do so (i.e., production is induced after the transfectedcells are produced but before implantation or after implantation). DNAencoding the desired product can, of course, be introduced into cells insuch a manner that it is expressed upon introduction (i.e., withoutinduction).

As taught herein, gene targeting can be used to replace a gene'sexisting regulatory region with a regulatory sequence isolated from adifferent gene or a novel regulatory sequence synthesized by geneticengineering methods. Such regulatory sequences can be comprised ofpromoters, enhancers, scaffold-attachment regions, negative regulatoryelements, transcriptional initiation sites, regulatory protein bindingsites or combinations of said sequences. (Alternatively, sequences whichaffect the structure or stability of the RNA or protein produced can bereplaced, removed, added, or otherwise modified by targeting, thesesequences including polyadenylation signals, mRNA stability elements,splice sites, leader sequences for enhancing or modifying transport orsecretion properties of the protein, or other sequences which alter orimprove the function or stability of protein or RNA molecules).According to this method, introduction of the exogenous DNA results indisablement of the endogenous sequences which control expression of theendogenous gene, either by replacing all or a portion of the endogenous(genomic) sequence or otherwise disrupting the function of theendogenous sequence. In the situation where targeting is used to replacea protein coding domain, chimeric, multifunctional proteins can beproduced which combine structural, enzymatic, or ligand or receptorbinding properties from two or more proteins into one polypeptide.

Selectable Markers

A variety of selectable markers can be incorporated into primary,secondary or immortalized cells. For example, a selectable marker whichconfers a selectable phenotype such as drug resistance, nutritionalauxotrophy, resistance to a cytotoxic agent or expression of a surfaceprotein, can be used. Selectable marker genes which can be used includeneo, gpt, dhfr, ada, pac, hyg, CAD, and hisD. The selectable phenotypeconferred makes it possible to identify and isolate recipient cells.Amplifiable genes encoding selectable markers (e.g., ada, dhfr and themultifunctional CAD gene which encodes carbamyl phosphate synthase,aspartate transcarbamylase, and dihydro-orotase) have the addedcharacteristic that they enable the selection of cells containingamplified copies of the selectable marker inserted into the genome. Thisfeature provides a mechanism for significantly increasing the copynumber of an adjacent or linked gene for which amplification isdesirable.

Selectable markers can be divided into two categories: positivelyselectable and negatively selectable (in other words, markers for eitherpositive selection or negative selection). In positive selection, cellsexpressing the positively selectable marker are capable of survivingtreatment with a selective agent (such as neo, gpt, dhfr, ada, pac, hyg,mdrl and hisD). In negative selection, cells expressing the negativelyselectable marker are destroyed in the presence of the selective agent(e.g., tk, gpt).

DNA Constructs

DNA constructs, which include exogenous DNA and, optionally, DNAencoding a selectable marker, along with additional sequences necessaryfor expression of the exogenous DNA in recipient cells, are used totransfect primary, secondary or immortalized cells in which the encodedproduct is to be produced. The DNA construct can also include targetingsequences for homologous recombination with host cell DNA. DNAconstructs which include exogenous DNA sequences which do not encode agene product (and are the therapeutic product) and, optionally, includeDNA encoding a selectable marker, can be used to transfect primary,secondary or immortalized cells. The DNA constructs may be introducedinto cells by a variety of methods, including electroporation,microinjection, calcium phosphate precipitation, and liposome-polybrene- or DEAE dextran-mediated transfection. Alternatively,infectious vectors, such as retroviral, herpes, adenovirus,adenovirus-associated, mumps and poliovirus vectors, can be used tointroduce the DNA.

In one embodiment, the DNA construct includes exogenous DNA and one ormore targeting sequences, generally located at both ends of theexogenous DNA sequence. Targeting sequences are DNA sequences normallypresent in the genome of the cells as obtained (e.g., an essential gene,a nonessential gene or noncoding DNA, or sequences present in the genomethrough a previous modification). Such a construct is useful tointegrate exogenous DNA (at a preselected cite in a recipient cell isgenome) encoding a therapeutic product, such as a hormone, a cytokine,an antigen, an antibody, an enzyme, a clotting factor, a transportprotein, a receptor, a regulatory protein, a structural protein, ananti-sense RNA, a ribozyme or a protein or a nucleic acid which does notoccur in nature. In particular, exogenous DNA can encode one of thefollowing: Factor VIII, Factor IX, erythropoietin, alpha-1 antitrypsin,calcitonin, glucocerebrosidase, growth hormone, low density lipoprotein(LDL) receptor, apolipoproteins (e.g. apolipoprotein E or apolipoproteinA-I), IL-2 receptor and its antagonists, insulin, globin,immunoglobulins, catalytic antibodies, the interleukins, insulin-likegrowth factors, superoxide dismutase, immune responder modifiers,parathyroid hormone, interferons, nerve growth factors, tissueplasminogen activators, and colony stimulating factors, and variants ofthese proteins which have improved or novel biological properties ormore desirable half-life or turnover times in vivo Such a construct isalso useful to integrate exogenous DNA (at a preselected site in arecipient cell's genome) which is a therapeutic product, such as DNAsequences sufficient for sequestration of a protein or nucleic acid inthe transfected primary or secondary cell, DNA sequences which bind to acellular regulatory protein, DNA sequences which alter the secondary ortertiary chromosomal structure and DNA sequences which aretranscriptional regulatory elements into genomic DNA of primary orsecondary cells.

The exogenous DNA, targeting sequences and selectable marker can beintroduced into cells on a single DNA construct or on separateconstructs. The total length of the DNA construct will vary according tothe number of components (exogenous DNA, targeting sequences, selectablemarker gene) and the length of each. The entire construct length willgenerally be at least 20 nucleotides. In a construct in which theexogenous DNA has sufficient homology with genomic DNA to undergohomologous recombination, the construct will include a single component,the exogenous DNA. In this embodiment, the exogenous DNA, because of itshomology, serves also to target integration into genomic DNA andadditional targeting sequences are unnecessary. Such a construct isuseful to knock out, replace or repair a resident DNA sequence, such asan entire gene, a gene portion, a regulatory element or portion thereofor regions of DNA which, when removed, place regulatory and structuralsequences in functional proximity. It is also useful when the exogenousDNA contains a marker useful for selection or amplification of linkedsequences.

In a second embodiment, the DNA construct includes exogenous DNA,targeting DNA sequences and DNA encoding at least one selectable marker.In this second embodiment, the order of construct components can be:targeting sequences-exogenous DNA-DNA encoding a selectablemarker(s)-targeting sequences. In this embodiment, one or moreselectable markers are included in the construct, which makes selectionbased on a selectable phenotype possible. Cells that stably integratethe construct will survive treatment with the selective agent; a subsetof the stably transfected cells will be HR cells, which can beidentified by a variety of techniques, including PCR, Southernhybridization and phenotypic screening.

In a third embodiment, the order of components in the DNA construct canbe: targeting sequence—selectable marker 1—targeting sequence—selectablemarker 2. In this embodiment selectable marker 2 displays the propertyof negative selection. That is, the gene product of selectable marker 2can be selected against by growth in an appropriate media formulationcontaining an agent (typically a drug or metabolite analog) which killscells expressing selectable marker 2. Recombination between thetargeting sequences flanking selectable marker 1 with homologoussequences in the host cell genome results in the targeted integration ofselectable marker 1, while selectable marker 2 is not integrated. Suchrecombination events generate cells which are stably transfected withselectable marker 1 but not stably transfected with selectable marker 2,and such cells can be selected for by growth in the media containing theselective agent which selects for selectable marker 1 and the selectiveagent which selects against selectable marker 2.

A DNA construct can include an inducible promoter which controlsexpression of the exogenous DNA, making inducible expression possible.optionally, the DNA construct can include a bacterial origin ofreplication and bacterial antibiotic resistance markers, which allow forlarge-scale plasmid propagation in bacteria. A DNA construct whichincludes DNA encoding a selectable marker, along with additionalsequences, such as a promoter, polyadenylation site and splicejunctions, can be used to confer a selectable phenotype upon transfectedprimary or secondary cells (e.g., plasmid pcDNEO, schematicallyrepresented in FIG. 2). Such a DNA construct can be co-transfected intoprimary or secondary cells, along with a targeting DNA sequence, usingmethods described herein.

In all embodiments of the DNA construct, exogenous DNA can encode one ormore products, can be one or more therapeutic products or one or more ofeach, thus making it possible to deliver multiple products.

Uses of Transfected Cells

Cells produced using the methods and DNA constructs described herein canbe used for a wide variety of purposes. Primary, secondary, orimmortalized cells of vertebrate origin can be produced in which 1) DNAalready present in a recipient cell is repaired, altered, deleted, orreplaced; 2) a gene or DNA sequence which encodes a therapeutic product(or other desired product) or is itself a therapeutic product isintroduced into the genome of a recipient cell at a preselected site(i.e. gene targeting); 3) regulatory sequences present in the primary,secondary or immortalized cell recipients have been repaired, altered,deleted or replaced; or 4) an entire gene or gene portion has beenrepaired, altered, deleted, or replaced. Homologous recombination canalso be used to produce universal donor cells, in which cell surfacemarkers involved in histocompatibility have been altered, deleted orreplaced, or in which the expression of such markers is altered,impaired, or eliminated.

The cells of the present invention are useful for in vitro production oftherapeutic products which can be purified and delivered by conventionalpharmaceutic routes. For example, primary, secondary, or immortalizedhuman cells can be transfected with exogenous DNA containing aregulatory region which, upon homologous recombination with genomic DNAsequences, results in the replacement of an endogenous target gene'sregulatory region with a regulatory region that allows novel expressionand/or regulation of the target gene and, ultimately, production of atherapeutically useful product by the transfected cell. The activatedendogenous target gene can further be amplified if an appropriateselectable marker gene is included in the targeting DNA. With or withoutamplification, these cells can be subject to large-scale cultivation forharvest of intracellular or extracellular protein products.

Transfected cells of the present invention are useful, as populations oftransfected primary cells, transfected clonal cell strains, transfectedheterogenous cell strains, and as cell mixtures in which at least onerepresentative cell of one of the three preceding categories oftransfected cells is present, as a delivery system for treating anindividual with an abnormal or undesirable condition which responds todelivery of a therapeutic product, which is either: 1) a therapeuticprotein (e.g., a protein which is absent, underproduced relative to theindividual's physiologic needs, defective or inefficiently orinappropriately utilized in the individual; a protein with novelfunctions, such as enzymatic or transport functions) or 2) a therapeuticnucleic acid (e.g., DNA which binds to or sequesters a regulatoryprotein, RNA which inhibits gene expression or has intrinsic enzymaticactivity). In the method of the present invention of providing atherapeutic protein or nucleic acid, transfected primary cells, clonalcell strains or heterogenous cell strains are administered to anindividual in whom the abnormal or undesirable condition is to betreated or prevented, in sufficient quantity and by an appropriateroute, to express or make available the exogenous DNA at physiologicallyrelevant levels. A physiologically relevant level is one which eitherapproximates the level at which the product is produced in the body orresults in improvement of the abnormal or undesirable condition. Cellsadministered in the present method are cells transfected with exogenousDNA which encodes a therapeutic product, exogenous DNA which is itself atherapeutic product or exogenous DNA, such as a regulatory sequence,which is introduced into a preselected site in genomic DNA throughhomologous recombination and functions to cause recipient cells toproduce a product which is normally not expressed in the cells or toproduce the product of a higher level than occurs in the correspondingnontransfected cell. In the embodiment in which a regulatory sequence(e.g., a promoter) is introduced, it replaces or disables a regulatorysequence normally associated with a gene, and results in expression ofthe gene at a higher level than occurs in the correspondingnontransfected cell or allows a pattern of regulation or induction thatis different from the corresponding nontransfected cell.

Immortalized cells which produce a therapeutic protein produced by themethods described herein and in the related U.S. patent application Ser.Nos. 07/789,188, 07,911,533 and 07,787,840 (incorporated herein byreference), can be used in gene therapy whether made by cells producedby: 1) random integration of the therapeutic protein, 2) homologousrecombination to target the therapeutic protein into a cell's genome, 3)homologous recombination to activate or turn on a gene of therapeuticinterest, or 4) gene amplification in conjunction with one of the threepreceding methods. According to the invention described herein, theimmortalized cells are enclosed in one of a number of semipermeablebarrier devices. The permeability properties of the device are such thatthe cells are prevented from leaving the device upon implantation intoan animal, but the therapeutic product is freely permeable and can leavethe barrier device and enter the local space surrounding the implant orenter the systemic circulation. A number of filtration membranes can beused for this purpose, including, but not limited to, cellulose,cellulose acetate, nitrocellulose, polysulfone, polyvinylidenedifluoride, polyvinyl chloride polymers and polymers of polyvinylchloride derivatives. Alternatively, barrier devices can be utilized toallow primary, secondary, or immortalized cells from another species tobe used for gene therapy in humans. The use of cells from other speciescan be desirable in cases where the non-human cells are advantageous forprotein production purposes or in cases where the non-human protein istherapeutically useful, for example, the use of cells derived fromsalmon for the production of salmon calcitonin and the use of cellsderived from pigs for the production of porcine insulin.

Cells from non-human species can also be used for in vitro proteinproduction. These cells can be immortalized, primary, or secondary cellswhich produce a therapeutic protein produced by the methods describedhere and in the U.S. patent applications incorporated herein byreference, whether made by cells produced by: 1) random integration ofthe therapeutic protein, 2) homologous recombination to target thetherapeutic protein into a cell's genome, 3) homologous recombination toactivate or turn on a gene of therapeutic interest, or 4) geneamplification in conjunction with one of the three preceding methods.The use of cells from other species may be desirable in cases where thenon-human cells are advantageous for protein production purposes (forexample CHO cells) or in cases where the non-human protein istherapeutically or commercially useful, for example, the use of cellsderived from salmon for the production of salmon calcitonin, the use ofcells derived from pigs for the production of porcine insulin, and theuse of bovine cells for the production of bovine growth hormone.

Transfected cells of the present invention are useful in a number ofapplications in humans and animals. In one embodiment, the cells can beimplanted into a human or an animal for protein delivery in the human oranimal. For example, human growth hormone (hGH), human EPO (hEPO), orhuman insulinotropin can be delivered systemically in humans fortherapeutic benefits. Barrier devices, through which the therapeuticproduct is freely permeable, can be used to retain cells in a fixedposition in vivo or to protect and isolate the cells from the host'simmune system. Barrier devices are particularly useful and allowtransfected immortalized cells, transfected cells from another species(transfected xenogeneic cells), or cells from anonhistocompatibility-matched donor (transfected allogeneic cells) to beimplanted for treatment of human or animal conditions or foragricultural uses (i.e., meat and dairy production). Barrier devicesalso allow convenient short-term (i.e., transient) therapy by providingready access to the cells for removal when the treatment regimen is tobe halted for any reason.

Transfected cells of the present invention are also useful for elicitingantibody production or for immunizing humans and animals againstpathogenic agents. Implanted transfected cells can be used to deliverimmunizing antigens that result in stimulation of the host's cellularand humoral immune responses. These immune responses can be designed forprotection of the host from future infectious agents (i.e., forvaccination), to stimulate and augment the disease-fighting capabilitiesdirected against an ongoing infection, or to produce antibodies directedagainst the antigen produced in vivo by the transfected cells that canbe useful for therapeutic or diagnostic purposes. Removable barrierdevices can be used to allow a simple means of terminating exposure tothe antigen. Alternatively, the use of cells that will ultimately berejected (xenogeneic or allogeneic transfected cells) can be used tolimit exposure to the antigen since antigen production will cease whenthe cells have been rejected.

Explanation of the Examples

As described herein, Applicants have demonstrated that DNA can beintroduced into primary, secondary or immortalized vertebrate cells andintegrated into the genome of the transfected primary or secondary cellsby homologous recombination. That is, they have demonstrated genetargeting in primary, secondary and immortalized mammalian cells. Theyhave further demonstrated that the exogenous DNA has the desiredfunction in the homologously recombinant (HR) cells and that correctlytargeted cells can be identified on the basis of a detectable phenotypeconferred by the properly targeted DNA.

In addition, the present invention relates to a method of proteinproduction using transfected primary, secondary or immortalized cells.The method involves transfecting primary cells, secondary cells orimmortalized cells with exogenous DNA which encodes a therapeuticproduct or with DNA which is sufficient to target to and activate anendogenous gene which encodes a therapeutic product. For example,Examples 1g, 1j, 2, 3 and 4 describe protein production by targeting andactivation of a selected endogenous gene.

The applicants also describe DNA constructs and methods for amplifyingan endogenous cellular gene that has been activated by gene targeting(Examples 1f-1k and Example 3) and further describe methods by which agene can be inserted at a preselected site in the genome of a primary,secondary, or immortalized cell by gene targeting (Example 1d).

Applicants describe construction of a plasmid useful for targeting to aparticular locus (the HPRT locus) in the human genome and selectionbased upon a drug resistant phenotype (Example 1a). This plasmid isdesignated pE3Neo and its integration into the cellular genomes at theHPRT locus produces cells which have an hprt⁻, 6-TG resistant phenotypeand are also G418 resistant. As described, they have shown that pE3Neofunctions properly in gene targeting in an established human fibroblastcell line (Example 1b), by demonstrating localization of the DNAintroduced into established cells within exon 3 of the HPRT gene.

In addition, Applicants demonstrate gene targeting in primary andsecondary human skin fibroblasts using pE3Neo (Example 1c). The subjectapplication further demonstrates that modification of DNA terminienhances targeting of DNA into genomic DNA (Examples 1c and 1e).

Examples 1f-1h and 2 illustrate embodiments in which the normalregulatory sequences upstream of the human EPO gene are altered to allowexpression of hEPO in primary or secondary fibroblast strains which donot express EPO in detectable quantities in their untransfected state.In one embodiment the product of targeting leaves the normal EPO proteinintact, but under the control of the mouse metallothionein promoter.Examples 1i and 1j demonstrate the use of similar targeting constructsto activate the endogenous growth hormone gene in primary or secondaryhuman fibroblasts. In other embodiments described for activating EPOexpression in human fibroblasts, the products of targeting events arechimeric transcription units, in which the first exon of the humangrowth hormone gene is positioned upstream of EPO exons 2-5. The productof transcription (controlled by the mouse metallothionein promoter),splicing, and translation is a protein in which amino acids 1-4 of thehEPO signal peptide are replaced with amino acid residues 1-3 of hGH.The chimeric portion of this protein, the signal peptide, is removedprior to secretion from cells. Example 5 describes targeting constructsand methods for producing cells which will convert a gene (with introns)into an expressible cDNA copy of that gene (without introns) and therecovery of such expressible cDNA molecules in microbial (e.g., yeast orbacterial) cells.

The Examples provide methods for activating or for activating andamplifying endogenous genes by gene targeting which do not requiremanipulation or other uses of the target genes' protein coding regions.By these methods, normally inactive genes can be activated in cells thathave properties desirable for in vitro protein production (e.g.,pharmaceutics) or in vivo protein delivery methods (e.g. gene therapy).FIGS. 5 and 6 illustrate two strategies for transcriptionally activatingthe hEPO gene.

Using the methods and DNA constructs or plasmids taught herein ormodifications thereof which are apparent to one of ordinary skill in theart, exogenous DNA which encodes a therapeutic product (e.g., protein,ribozyme, nucleic acid) can be inserted at preselected sites in thegenome of vertebrate (e.g., mammalian, both human and nonhuman) primaryor secondary cells.

The present invention will now be illustrated by the following examples,which are not intended to be limiting in any way.

EXAMPLES Example 1 Production of Transfected Cell Strains by GeneTargeting

Gene targeting occurs when transfecting DNA either integrates into orpartially replaces chromosomal DNA sequences through a homologousrecombinant event. While such events can occur in the course of anygiven transfection experiment, they are usually masked by a vast excessof events in which plasmid DNA integrates by nonhomologous, orillegitimate, recombination.

Examples 1a, 1b, 1e, 1f and 1i are reproduced from U.S. patentapplication Ser. No. 07/789,188, filed on Nov. 5, 1991, and incorporatedherein by reference. These examples are presented here for backgroundinformation.

a. Generation of a Construct Useful for Selection of Gene TargetingEvents in Human Cells

One approach to selecting the targeted events is by genetic selectionfor the loss of a gene function due to the integration of transfectingDNA. The human HPRT locus encodes the enzyme hypoxanthine-phosphoribosyltransferase. hprt⁻ cells can be selected for by growth in mediumcontaining the nucleoside analog 6-thioguanine (6-TG): cells with thewild-type (HPRT+) allele are killed by 6-TG, while cells with mutant(hprt⁻) alleles can survive. Cells harboring targeted events whichdisrupt HPRT gene function are therefore selectable in 6-TG medium.

To construct a plasmid for targeting to the HPRT locus, the 6.9 kbHindIII fragment extending from positions 11,960-18,869 in the HPRTsequence (Genebank name HUMHPRTB; Edwards, A. et al., Genomics 6:593-608(1990)) and including exons 2 and 3 of the HPRT gene, is subcloned intothe HindIII site of pUC12. The resulting clone is cleaved at the uniqueXhoI site in exon 3 of the HPRT gene fragment and the 1.1 kb SalI-XhoIfragment containing the neo gene from pMC1Neo (Stratagene) is inserted,disrupting the coding sequence of exon 3. One orientation, with thedirection of neo transcription opposite that of HPRT transcription waschosen and designated pE3Neo. The replacement of the normal HPRT exon 3with the neo-disrupted version will result in an hprt⁻, 6-TG resistantphenotype. Such cells will also be G418 resistant.

b. Gene Targeting in an Established Human Fibroblast Cell Line

As a demonstration of targeting in immortalized cell lines, and toestablish that pE3Neo functions properly in gene targeting, the humanfibrosarcoma cell line HT1080 (ATCC CCL 121) was transfected with pE3Neoby electroporation.

HT1080 cells were maintained in HAT (hypoxanthine/aminopterin/xanthine)supplemented DMEM with 15% calf serum (Hyclone) prior toelectroporation. Two days before electroporation, the cells are switchedto the same medium without aminopterin. Exponentially growing cells weretrypsinized and diluted in DMEM/15% calf serum, centrifuged, andresuspended in PBS (phosphate buffered saline) at a final cell volume of13.3 million cells per ml. pE3Neo is digested with HindIII, separatingthe 8 kb HPRT-neo fragment from the pUC12 backbone, purified by phenolextraction and ethanol precipitation, and resuspended at a concentrationof 600 μg/ml. 50 μl (30 μg) was added to the electroporation cuvette(0.4 cm electrode gap; Bio-Rad Laboratories), along with 750 μl of thecell suspension (10 million cells). Electroporation was at 450 volts,250 μFarads (Bio-Rad Gene Pulser; Bio-Rad Laboratories). The contents ofthe cuvette were immediately added to DMEM with 15% calf serum to yielda cell suspension of 1 million cells per 25 ml media. 25 ml of thetreated cell suspension was plated onto 150 mm diameter tissue culturedishes and incubated at 37° C, 5% CO₂. 24 hrs later, a G418 solution wasadded directly to the plates to yield a final concentration of 800 μg/mlG418. Five days later the media was replaced with DMEM/15% calfserum/800 μg/ml G418. Nine days after electroporation, the media wasreplaced with DMEM/15% calf serum/800 μg/ml G418 and 10 μM6-thioguanine. Colonies resistant to G418 and 6-TG were picked usingcloning cylinders 14-16 days after the dual selection was initiated.

The results of five representative targeting experiments in HT1080 cellsare shown in Table 1.

TABLE 1 Number of Number of G418^(r) Transfection Treated Cells 6-TG^(r)Clones 1 1 × 10⁷ 32 2 1 × 10⁷ 28 3 1 × 10⁷ 24 4 1 × 10⁷ 32 5 1 × 10⁷ 66

For transfection 5, control plates designed to determine the overallyield of G418^(r) colonies indicated that 33,700 G418^(r) colonies couldbe generated from the initial 1×10⁷ treated cells. Thus, the ratio oftargeted to non-targeted events is 66/33,700, or 1 to 510. In the fiveexperiments combined, targeted events arise at a frequency of 3.6×10⁶,or 0.00036% of treated cells.

Restriction enzyme and Southern hybridization experiments using probesderived from the neo and HPRT genes localized the neo gene to the HPRTlocus at the predicted site within HPRT exon 3.

c. Gene Targeting in Primary and Secondary Human Skin Fibroblasts

pE3Neo is digested with HindIII, separating the 8 kb HPRT-neo fragmentfrom the pUC12 backbone, and purified by phenol extraction and ethanolprecipitation. DNA was resuspended at 2 mg/ml. Three million secondaryhuman foreskin fibroblasts cells in a volume of 0.5 ml wereelectroporated at 250 volts and 960 μgFarads, with 100 μg of HindIIIpE3Neo (50 μl). Three separate transfections were performed, for a totalof 9 million treated cells. Cells are processed and selected for G418resistance. 500,000 cells per 150 mm culture dish were plated for G418selection. After 10 days under selection, the culture medium is replacedwith human fibroblast nutrient medium containing 400 μg/ml G418 and 10μM 6-TG. Selection with the two drug combination is continued for 10additional days. Plates are scanned microscopically to localize humanfibroblast colonies resistant to both drugs. The fraction of G418^(r)t-TG^(r) colonies is 4 per 9 million treated cells. These coloniesconstitute 0.0001% (or 1 in a million) of all cells capable of formingcolonies. Control plates designed to determine the overall yield ofG418^(r) colonies indicated that 2,850 G418^(r) colonies could begenerated from the initial 9×10⁶ treated cells. Thus, the ratio oftargeted to non-targeted events is 4/2,850, or 1 to 712. Restrictionenzyme and Southern hybridization experiments using probes derived fromthe neo and HPRT genes were used to localize the neo gene to the HPRTlocus at the predicted site within HPRT exon 3 and demonstrate thattargeting had occurred in these four clonal cell strains. Coloniesresistant to both drugs have also been isolated by transfecting primarycells (1/3.0×10⁷).

The results of several pE3Neo targeting experiments are summarized inTable 2. HindIII digested pE3Neo was either transfected directly ortreated with exonuclease III to generate 5′ single-stranded overhangsprior to transfection (see Example 1c). DNA preparations withsingle-stranded regions ranging from 175 to 930 base pairs in lengthwere tested. Using pE3neo digested with HindIII alone, 1/799G418-resistant colonies were identified by restriction enzyme andSouthern hybridization analysis as having a targeted insertion of theneo gene at the HPRT locus (a total of 24 targeted clones wereisolated). Targeting was maximally stimulated (approximately 10-foldstimulation) when overhangs of 175 bp were used, with 1/80 G418^(r)colonies displaying restriction fragments that are diagnostic fortargeting at HPRT (a total of 9 targeted clones were isolated). Thus,using the conditions and recombinant DNA constructs described here,targeting is readily observed in normal human fibroblasts and theoverall targeting frequency (the number of targeted clones divided bythe total number of clones stably transfected to G418-resistance) can bestimulated by transfection with targeting constructs containingsingle-stranded overhanging tails, by the method as described in Example1e.

TABLE 2 TARGETING TO THE HPRT LOCUS IN HUMAN FIBROBLASTS pE3neo Numberof Number Targeted Total Number of Treatment Experiments Per G418^(r)Colony Targeted Clone HindIII digest 6 1/799 24 175 bp overhang 1 1/80 9 350 bp overhang 3 1/117 20 930 bp overhang 1 1/144 1

d. Generation of a Construct for Targeted Insertion of a Gene ofTherapeutic Interest Into the Human Genome and Its Use in Gene Targeting

A variant of pE3Neo, in which a gene of therapeutic interest is insertedwithin the HPRT coding region, adjacent to or near the neo gene, can beused to target a gene of therapeutic interest to a specific position ina recipient primary or secondary cell genome. Such a variant of pE3Neocan be constructed for targeting the hGH gene to the HPRT locus.

pXGH5 (schematically presented in FIG. 1) is digested with EcoRI and the4.1 kb fragment containing the hGH gene and linked mouse metallothionein(mMT) promoter is isolated. The EcoRI overhangs are filled in with theKlenow fragment from E. coli DNA polymerase. Separately, pE3Neo isdigested with XhoI, which cuts at the junction of the neo fragment andHPRT exon 3 (the 3′ junction of the insertion into exon 3). The XhoIoverhanging ends of the linearized plasmid are filled in with the Klenowfragment from E. coli DNA polymerase, and the resulting fragment isligated to the 4.1 kb blunt-ended hGH-mMT fragment. Bacterial coloniesderived from the ligation mixture are screened by restriction enzymeanalysis for a single copy insertion of the hGH-mMT fragment and oneorientation, the hGH gene transcribed in the same direction as the neogene, is chosen and designated pE3Neo/hGH. pE3Neo/hGH is digested withHindIII, releasing the 12.1 kb fragment containing HPRT, neo and mMT-hGHsequences. Digested DNA is treated and transfected into primary orsecondary human fibroblasts as described in Example 1c. G418^(r) TG^(r)colonies are selected and analyzed for targeted insertion of the mMT-hGHand neo sequences into the HPRT gene as described in Example 1c.Individual colonies are assayed for hGH expression using a commerciallyavailable immunoassay (Nichols Institute).

Secondary human fibroblasts were transfected with pE3Neo/hGH andthioguanine-resistant colonies were analyzed for stable hGH expressionand by restriction enzyme and Southern hybridization analysis. Ofthirteen TG^(r) colonies analyzed, eight colonies were identified withan insertion of the hGH gene into the endogenous HPRT locus. All eightstrains stably expressed significant quantities of hGH, with an averageexpression level of 22.7 μg/10⁶ cells/24 hours. Alternatively, plasmidpE3neoEPO, FIG. 4, may be used to target EPO to the human HPRT locus.

The use of homologous recombination to target a gene of therapeuticinterest to a specific position in a cell's genomic DNA can be expandedupon and made more useful for producing products for therapeuticpurposes (e.g., pharmaceutics, gene therapy) by the insertion of a genethrough which cells containing amplified copies of the gene can beselected for by exposure of the cells to an appropriate drug selectionregimen. For example, pE3neo/hGH (Example 1d) can be modified byinserting the dhfr, ada, or CAD gene at a position immediately adjacentto the hGH or neo genes in pE3neo/hGH. Primary, secondary, orimmortalized cells are transfected with such a plasmid and correctlytargeted events are identified. These cells are further treated withincreasing concentrations of drugs appropriate for the selection ofcells containing amplified genes (for dhfr, the selective agent ismethotrexate, for CAD the selective agent isN-(phosphonacetyl)-L-aspartate (PALA), and for ada the selective agentis an adenine nucleoside (e.g., alanosine). In this manner theintegration of the gene of therapeutic interest will be coamplifiedalong with the gene for which amplified copies are selected. Thus, thegenetic engineering of cells to produce genes for therapeutic uses canbe readily controlled by preselecting the site at which the targetingconstruct integrates and at which the amplified copies reside in theamplified cells.

e. Modification of DNA Termini to Enhance Targeting

Several lines of evidence suggest that 3′-overhanging ends are involvedin certain homologous recombination pathways of E. coli, bacteriophage,S. cerevisiae and Xenopus laevis. In Xenopus laevis oocytes, moleculeswith 3′-overhanging ends of several hundred base pairs in lengthunderwent recombination with similarly treated molecules much morerapidly after microinjection than molecules with very short overhangs (4bp) generated by restriction enzyme digestion. In yeast, the generationof 3′-overhanging ends several hundred base pairs in length appears tobe a rate limiting step in meiotic recombination. No evidence for aninvolvement of 3′-overhanging ends in recombination in human cells hasbeen reported, and in no case have modified DNA substrates of any sortbeen shown to promote targeting (one form of homologous recombination)in any species. In human cells, the effect of 3′-overhanging ends ontargeting is untested. The experiment described in the following exampleand Example 1c suggests that 5′-overhanging ends are effective forstimulating targeting in primary, secondary and immortalized humanfibroblasts.

There have been no reports on the enhancement of targeting by modifyingthe ends of the transfecting DNA molecules. This example serves toillustrate that modification of the ends of linear DNA molecules, byconversion of the molecules' termini from a double-stranded form to asingle-stranded form, can stimulate targeting into the genome of primaryand secondary human fibroblasts.

1100 μg of plasmid pE3Neo (Example 1a) is digested with HindIII. ThisDNA can be used directly after phenol extraction and ethanolprecipitation, or the 8 kb HindIII fragment containing only HPRT and theneo gene can be separated away from the pUC12 vector sequences by gelelectrophoresis. ExoIII digestion of the HindIII digested DNA results inextensive exonucleolytic digestion at each end, initiating at each free3′ end, and leaving 5′-overhanging ends. The extent of exonucleolyticaction and, hence, the length of the resulting 5′-overhangs, can becontrolled by varying the time of ExoIII digestion. ExoIII digestion of100 μg of HindIII digested pE3Neo is carried out according to thesupplier's recommended conditions, for times of 30 sec, 1 min, 1.5 min,2 min, 2.5 min, 3 min, 3.5 min, 4 min, 4.5 min, and 5 min. To monitorthe extent of digestion an aliquot from each time point, containing 1 μgof ExoIII treated DNA, is treated with mung bean nuclease (Promega),under conditions recommended by the supplier, and the samplesfractionated by gel electrophoresis. The difference in size betweennon-treated, HindIII digested pE3Neo and the same molecules treated withExoIII and mung bean nuclease is measured. This size difference dividedby two gives the average length of the 5′-overhang at each end of themolecule. Using the time points described above and digestion at 30°,the 5′-overhangs produced should range from 100 to 1,000 bases.

60 μg of ExoIII treated DNA (total HindIII digest of pE3Neo) from eachtime point is purified and electroporated into primary, secondary, orimmortalized human fibroblasts under the conditions described in Example1c. The degree to which targeting is enhanced by each ExoIII treatedpreparation is quantified by counting the number of G418^(r) 6-TG^(r)colonies and comparing these numbers to targeting with HindIII digestedpE3Neo that was not treated with ExoIII.

The effect of 3′-overhanging ends can also be quantified using ananalogous system. In this case HindIII digested pE3Neo is treated withbacteriophage T7 gene 6 exonuclease (United States Biochemicals) forvarying time intervals under the supplier's recommended conditions.Determination of the extent of digestion (average length of 3′-overhangproduced per end) and electroporation conditions are as described forExoIII treated DNA. The degree to which targeting is enhanced by each T7gene 6 exonuclease treated preparation is quantified by counting thenumber of G418^(r) 6-TG^(r) colonies and comparing these numbers totargeting with HindIII digested pE3Neo that was not treated with T7 gene6 exonuclease.

Other methods for generating 5′ and 3′ overhanging ends are possible,for example, denaturation and annealing of two linear molecules thatpartially overlap with each other will generate a mixture of molecules,each molecule having 3′-overhangs at both ends or 5′-overhangs at bothends, as well as reannealed fragments indistinguishable from thestarting linear molecules. The length of the overhangs is determined bythe length of DNA that is not in common between the two DNA fragments.

f. Construction of Targeting Plasmids for Placing the HumanErythropoietin Gene Under the Control of the Mouse MetallothioneinPromoter in Primary, Secondary and Immortalized Human Fibroblasts

The following serves to illustrate one embodiment of the presentinvention, in which the normal positive and negative regulatorysequences upstream of the human erythropoietin (EPO) gene are altered toallow expression of human erythropoietin in primary, secondary orimmortalized human fibroblasts, which do not express EPO in significantquantities as obtained.

A region lying exclusively upstream of the human EPO coding region canbe amplified by PCR. Three sets of primers useful for this purpose weredesigned after analysis of the published human EPO [Genbank designationHUMERPA; Lin, F-K., et al., Proc. Natl. Acad. Sci., USA 82:7580-7584(1985)]. These primer pairs can amplify fragments of 609, 603, or 590bp.

TABLE 3 HUMERPA Fragment Primer Coordinate Sequence Size F1  2→205′AGCTTCTGGGCTTCCAGAC (SEQ ID NO 1) R2 610→595 5′GGGGTCCCTCAGCGAC 609 bp(SEQ ID NO 2) F2  8→24 5′TGGGCTTCCAGACCCAG (SEQ ID NO 3) R2 610→5955′GGGGTCCCTCAGCGAC 603 bp (SEQ ID NO 2) F3 21→40 5′CCAGCTACTTTGCGGAACTC(SEQ ID NO 4) R2 610→595 5′GGGGTCCCTCAGCGAC 590 bp (SEQ ID NO 2)

The three fragments overlap substantially and are interchangeable forthe present purposes. The 609 bp fragment, extending from −623 to −14relative to the translation start site (HUMERPA nucleotide positions 2to 610), is ligated at both ends with ClaI linkers. The resultingClaI-linked fragment is digested with ClaI and inserted into the ClaIsite of pBluescriptIISK/+ (Stratagene), with the orientation such thatHUMERPA nucleotide position 610 is adjacent to the SalI site in theplasmid polylinker). This plasmid, p5′EPO, can be cleaved, separately,at the unique FspI or SfiI sites in the EPO upstream fragment (HUMERPAnucleotide positions 150 and 405, respectively) and ligated to the mousemetallothionein promoter. Typically, the 1.8 kb EcoRI-BglII from themMT-I gene [containing no mMT coding sequences; Hamer, D. H. and WallingM., J. Mol. Appl. Gen, 1:273 288 (1982); this fragment can also beisolated by known methods from mouse genomic DNA using PCR primersdesigned from analysis of mMT sequences available from Genbank; i.e.,MUSMTI, MUSMTIP, MUSMTIPRM] is made blunt-ended by known methods andligated with SfiI digested (also made blunt-ended) or FspI digestedp5′EPO. The orientations of resulting clones are analyzed and those inwhich the former mMT BglII site is proximal to the SalI site in theplasmid polylinker are used for targeting primary and secondary humanfibroblasts. This orientation directs mMT transcription towards HUMERPAnucleotide position 610 in the final construct. The resulting plasmidsare designated p5′EPO-mMTF and p5′EPO-mMTS for the mMT insertions in theFspI and SfiI sites, respectively.

Additional upstream sequences are useful in cases where it is desirableto modify, delete and/or replace negative regulatory elements orenhancers that lie upstream of the initial target sequence. In the caseof EPO, a negative regulatory element that inhibits EPO expression inextrahepatic and extrarenal tissues [Semenza, G. L. et al., Mol. Cell.Biol. 10:930-938 (1990)] can be deleted. A series of deletions withinthe 6 kb fragment are prepared. The deleted regions can be replaced withan enhancer with broad host-cell activity [e.g. an enhancer from theCytomegalovirus (CMV)].

The orientation of the 609 bp 5′EPO fragment in the pBluescriptIISK/+vector was chosen since the HUMERPA sequences are preceded on their 5′end by a BamHI (distal) and HindIII site (proximal). Thus, a 6 kbBamHI-HindIII fragment normally lying upstream of the 609 bp fragment(Semenza, G. L. et al., Mol. Cell. Biol. 10:930-938 (1990)) can beisolated from genomic DNA by known methods. For example, abacteriophage, cosmid, or yeast artificial chromosome library could bescreened with the 609 bp PCR amplified fragment as a probe. The desiredclone will have a 6 kb BamHI-HindIII fragment and its identity can beconfirmed by comparing its restriction map from a restriction map aroundthe human EPO gene determined by known methods. Alternatively,constructing a restriction map of the human genome upstream of the EPOgene using the 609 bp fragment as a probe can identify enzymes whichgenerate a fragment originating between HUMERPA coordinates 2 and 609and extending past the upstream BamHI site; this fragment can beisolated by gel electrophoresis from the appropriate digest of humangenomic DNA and ligated into a bacterial or yeast cloning vector. Thecorrect clone will hybridize to the 609 bp 5′EPO probe and contain a 6kb BamHI-HindIII fragment. The isolated 6 kb fragment is inserted in theproper orientation into p5′EPO, p5′EPO-mMTF, or p5′EPO-mMTS (such thatthe HindIII site is adjacent to HUMERPA nucleotide position 2).Additional upstream sequences can be isolated by known methods, usingchromosome walking techniques or by isolation of yeast artificialchromosomes hybridizing to the 609 bp 5′EPO probe.

The cloning strategies described above allow sequences upstream of EPOto be modified in vitro for subsequent targeted transfection of primary,secondary or immortalized human fibroblasts. The strategies describesimple insertions of the mMT promoter, as well as deletion of thenegative regulatory region, and deletion of the negative regulatoryregion and replacement with an enhancer with broad host-cell activity.

g. Targeting to Sequences Flanking the Human EPO Gene and Isolation ofTargeted Primary, Secondary and Immortalized Human Fibroblasts byScreening

For targeting, the plasmids are cut with restriction enzymes that freethe insert away from the plasmid backbone. In the case of p5′EPO-mMTS,HindIII and SalI digestion releases a targeting fragment of 2.4 kb,comprised of the 1.8 kb mMT promoter flanked on the 5′ and 3′ sides by405 bp and 204 base pairs, respectively, of DNA for targeting thisconstruct to the regulatory region of the EPO gene. This DNA or the 2.4kb targeting fragment alone is purified by phenol extraction and ethanolprecipitation and transfected into primary or secondary humanfibroblasts under the conditions described in Example 1c. Transfectedcells are plated onto 150 mm dishes in human fibroblast nutrient medium.48 hours later the cells are plated into 24 well dishes at a density of10,000 cells/cm² [approximately 20,000 cells per well; if targetingoccurs at a rate of 1 event per 10⁶ clonable cells (Example 1c, thenabout 50 wells would need to be assayed to isolate a single expressingcolony]. Cells in which the transfecting DNA has targeted to thehomologous region upstream of EPO will express EPO under the control ofthe mMT promoter. After 10 days, whole well supernatants are assayed forEPO expression using a commercially available immunoassay kit (Amgen).Clones from wells displaying EPO synthesis are isolated using knownmethods, typically by assaying fractions of the heterogenous populationsof cells separated into individual wells or plates, assaying fractionsof these positive wells, and repeating as needed, ultimately isolatingthe targeted colony by screening 96-well microtiter plates seeded at onecell per well. DNA from entire plate lysates can also be analyzed by PCRfor amplification of a fragment using a mMT specific primer inconjunction with a primer lying upstream of HUMERPA nucleotideposition 1. This primer pair should amplify a DNA fragment of a sizeprecisely predicted based on the DNA sequence. Positive plates aretrypsinized and replated at successively lower dilutions, and the DNApreparation and PCR steps repeated as needed to isolate targeted cells.

The targeting schemes herein described can also be used to activate hGHexpression in immortalized human cells (for example, HT1080 fibroblasts,HeLa cells, MCF-7 breast cancer cells, K-562 leukemia cells, KBcarcinoma cells or 2780AD ovarian carcinoma cells) for the purposes ofproducing hGH for conventional pharmaceutic delivery.

h. Targeting to Sequences Flanking the Human EPO Gene and Isolation ofTargeted Primary, Secondary and Immortalized Human Fibroblasts by aPositive or a Combined Positive/Negative Selection System

The strategy for constructing p5′EPO-mMTF, p5′EPO-mMTS, and derivativesof such with the additional upstream 6 kb BamHI-HindIII fragment can befollowed with the additional step of inserting the neo gene adjacent tothe mMT promoter. In addition, a negative selection marker, for example,gpt (from PMSG (Pharmacia) or another suitable source], can be insertedadjacent to the HUMERPA sequences in the pBluescriptIISK/+ polylinker.In the former case, G418^(r) colonies are isolated and screened by PCRamplification or restriction enzyme and Southern hybridization analysisof DNA prepared from pools of colonies to identify targeted colonies. Inthe latter case, G418^(r) colonies are placed in medium containing6-thioxanthine to select against the integration of the gpt gene[Besnard, C. et al., Mol. Cell. Biol. 7:4139-4141 (1987)]. In addition,the HSV-TK gene can be placed on the opposite side of the insert as gpt,allowing selection for neo and against both gpt and TK by growing cellsin human fibroblast nutrient medium containing 400 μg/ml G418, 100 μM6-thioxanthine, and 25 μg/ml gancyclovir. The double negative selectionshould provide a nearly absolute selection for true targeted events andSouthern blot analysis provides an ultimate confirmation.

The targeting schemes herein described can also be used to activate hEPOexpression in immortalized human cells (for example, HT1080 fibroblasts,HeLa cells, MCF-7 breast cancer cells, K-562 leukemia cells, KBcarcinoma cells or 2780AD ovarian carcinoma cells) for the purposes ofproducing hEPO for conventional pharmaceutic delivery.

i. Construction of Targeting Plasmids for Placing the Human GrowthHormone Gene Under the Control of the Mouse Metallothione in Promoter inPrimary, Secondary or Immortalized Human Fibroblasts

The following example serves to illustrate one embodiment of the presentinvention, in which the normal regulatory sequences upstream of thehuman growth hormone gene are altered to allow expression of humangrowth hormone in primary, secondary or immortalized human fibroblasts.

Targeting molecules similar to those described in Example if fortargeting to the EPO gene regulatory region are generated using clonedDNA fragments derived from the 5′ end of the human growth hormone Ngene. An approximately 1.8 kb fragment spanning HUMGHCSA (Genbank Entry)nucleotide positions 3787-5432 (the positions of two EcoNI sites whichgenerate a convenient sized fragment for cloning or for diagnosticdigestion of subclones involving this fragment) is amplified by PCRprimers designed by analysis of the HUMGHCSA sequence in this region.This region extends from the middle of hGH gene N intron 1 to anupstream position approximately 1.4 kb 5′ to the translational startsite. pUC12 is digested with EcoRI and BamHI, treated with Klenow togenerate blunt ends, and recircularized under dilute conditions,resulting in plasmids which have lost the EcoRI and BamHI sites. Thisplasmid is designated pUC12XEB. HindIII linkers are ligated onto theamplified hGH fragment and the resulting fragment is digested withHindIII and ligated to HindIII digested pUC12XEB. The resulting plasmid,pUC12XEB-5′hGH, is digested with EcoRI and BamHI, to remove a 0.5 kbfragment lying immediately upstream of the hGH transcriptionalinitiation site. The digested DNA is ligated to the 1.8 kb EcoRI-BglIIfrom the mMT-I gene [containing no mMT coding sequences; Hamer, D. H.and Walling, M., J. Mol. Appl. Gen. 1:273-288 (1982); the fragment canalso be isolated by known methods from mouse genomic DNA using PCRprimers designed from analysis of mMT sequences available from Genbank;i.e., MUSMTI, MUSMTIP, MUSMTIPRM]. This plasmid p5′hGH-mMT has the mMTpromoter flanked on both sides by upstream hGH sequences.

The cloning strategies described above allow sequences upstream of hGHto be modified in vitro for subsequent targeted transfection of primary,secondary or immortalized human fibroblasts. The strategy described asimple insertion of the mMT promoter. Other strategies can beenvisioned, for example, in which an enhancer with broad host-cellspecificity is inserted upstream of the inserted mMT sequence.

j. Targeting to Sequences Flanking the Human hGH Gene and Isolation ofTargeted Primary, Secondary and Immortalized Human Fibroblasts byScreening

For targeting, the plasmids are cut with restriction enzymes that freethe insert away from the plasmid backbone. In the case of p5′hGH-mMT,HindIII digestion releases a targeting fragment of 2.9 kb, comprised ofthe 1.8 kb mMT promoter flanked on the 5′ end 3′ sides by DNA fortargeting this construct to the regulatory region of the hGH gene. ThisDNA or the 2.9 kb targeting fragment alone is purified by phenolextraction and ethanol precipitation and transfected into primary orsecondary human fibroblasts under the conditions previously described inrelated U.S. patent application, Ser. Nos. 07/787,840 and 07/911,533.Transfected cells are plated onto 150 mm dishes in human fibroblastnutrient medium. 48 hours later the cells are plated into 24 well dishesat a density of 10,000 cells/cm² [approximately 20,000 cells per well;if targeting occurs at a rate of 1 event per 10⁶ clonable cells (Example1c), then about 50 wells would need to be assayed to isolate a singleexpressing colony]. Cells in which the transfecting DNA has targeted tothe homologous region upstream of hGH will express hGH under the controlof the mMT promoter. After 10 days, whole well supernatants are assayedfor hGH expression using a commercially available immunoassay kit(Nichols). Clones from wells displaying hGH synthesis are isolated usingknown methods, typically by assaying fractions of the heterogenouspopulations of cells separated into individual wells or plates, assayingfractions of these positive wells, and repeating as needed, ultimatelyisolated the targeted colony by screening 96-well microtiter platesseeded at one cell per well. DNA from entire plate lysates can also beanalyzed by PCR for amplification of a fragment using a mMT specificprimer in conjunction with a primer lying downstream of HUMGHCSAnucleotide position 5,432. This primer pair should amplify a DNAfragment of a size precisely predicted based on the DNA sequence.Positive plates are trypsinized and replated at successively lowerdilutions, and the DNA preparation and PCR steps repeated as needed toisolate targeted cells.

The targeting schemes herein described can also be used to activate hGHexpression in immortalized human cells (for example, HT1080 fibroblasts,HeLa cells, MCF-7 breast cancer cells, K-562 leukemia cells, KBcarcinoma cells or 2780AD ovarian carcinoma cells) for the purposes ofproducing hGH for conventional pharmaceutic delivery.

k. Targeting to Sequences Flanking the Human hGH Gene and Isolation ofTargeted Primary, Secondary and Immortalized Human Fibroblasts by aPositive or a Combined Positive/negative Selection System

The strategy for constructing p5′hGH-mMT can be followed with theadditional step of inserting the neo gene adjacent to the mMT promoter.In addition, a negative selection marker, for example, gpt [from pMSG(Pharmacia) or another suitable source], can be inserted adjacent to theHUMGHCSA sequences in the pUC12 poly-linker. In the former case,G418^(r) colonies are isolated and screened by PCR amplification orrestriction enzyme and Southern hybridization analysis of DNA preparedfrom pools of colonies to identify targeted colonies. In the lattercase, G418^(r) colonies are placed in medium containing thioxanthine toselect against the integration of the gpt gene (Besnard, C. at al., Mol.Cell. Biol. 7: 4139-4141 (1987)). In addition, the HSV-TK gene can beplaced on the opposite side of the insert as gpt, allowing selection forneo and against both gpt and TK by growing cells in human fibroblastnutrient medium containing 400 μg/ml G418, 100 μM 6-thioxanthine, and 25μg/ml gancyclovir. The double negative selection should provide a nearlyabsolute selection for true targeted events. Southern hybridizationanalysis is confirmatory.

The targeting schemes herein described can also be used to activate hGHexpression in immortalized human cells (for example, HT1080 fibroblasts,HeLa cells, MCF-7 breast cancer cells, K-562 leukemia cells, KBcarcinoma cells or 2780AD ovarian carcinoma cells) for the purposes ofproducing hGH for conventional pharmaceutic delivery.

The targeting constructs described in Examples 1f and 1i, and used inExamples 1g, 1h, 1j and 1k can be modified to include an amplifiableselectable marker (e.g., ada, dhfr, or CAD) which is useful forselecting cells in which the activated endogenous gene, and theamplifiable selectable marker, are amplified. Such cells, expressing orcapable of expressing the endogenous gene encoding a therapeutic productcan be used to produce proteins (e.g., hGH and hEPO) for conventionalpharmaceutic delivery or for gene therapy.

Example 2 Construction of Targeting Plasmids Which Result in ChimericTranscription Units in Which Human Growth Hormone and ErythropoietinSequences are Fused

The following serves to illustrate two further embodiments of thepresent invention, in which the normal regulatory sequences upstream ofthe human EPO gene are altered to allow expression of hEPO in primary orsecondary fibroblast strains which do not express EPO in detectablequantities in their untransfected state as obtained. In theseembodiments, the products of the targeting events are chimerictranscription units in which the first exon of the human growth hormonegene is positioned upstream of EPO exons 2-5. The product oftranscription, splicing and translation is a protein in which aminoacids 1-4 of the hEPO signal peptide are replaced with amino acidresidues 1-3 of hGH. The two embodiments differ with respect to both therelative positions of the foreign regulatory sequences that are insertedand the specific pattern of splicing that needs to occur to produce thefinal, processed transcript.

Plasmid pXEPO-10 is designed to replace exon 1 of hEPO with exon 1 ofhGH by gene targeting to the endogenous hEPO gene on human chromosome 7.Plasmid pXEPO-10 is constructed as follows. First, the intermediateplasmid pT163 is constructed by inserting the 6 kb HindIII-BamHIfragment (see Example if) lying upstream of the hEPO coding region intoHindIII-BamHI digested pBluescriptII SK+ (Stratagene, LaJola, Calif.).The product of this ligation is digested with XhoI and HindIII andligated to the 1.1 kb HindIII-XhoI fragment from pMClneoPolyA (Thomas,K. R. and Capecchi, M. R. Cell 51: 503-512 (1987) available fromStrategene, LaJola, Calif. to create pT163. Oligonucleotides 13.1-13.4are utilized in polymerase chain reactions to generate a fusion fragmentin which the mouse metallothionein 1 (mMT-I) promoter—hGH exon 1sequences are additionally fused to hEPO intron 1 sequences. First,oligonucleotides 13.1 and 13.2 are used to amplify the approximately0.73 kb mMT-I promoter—hGH exon 1 fragment from pXGH5 (FIG. 1). Next,oligonucleotides 13.3 and 13.4 are used to amplify the approximately0.57 kb fragment comprised predominantly of hEPO intron 1 from humangenomic DNA. Finally, the two amplified fragments are mixed and furtheramplified with oligonucleotides 13.1 and 13.4 to generate the finalfusion fragment (fusion fragment 3) flanked by a SalI site at the 5′side of the mMT-I moiety and an XhoI site at the 3′ side of the hEPOintron 1 sequence. Fusion fragment 3 is digested with XhoI and SalI andligated to XhoI digested pT163. The ligation mixture is transformed intoE. coli and a clone containing a single insert of fusion fragment 3 inwhich the XhoI site is regenerated at the 3′ side of hEPO intron 1sequences is identified and designated pXEPO-10.

13.1 5′ AAAAGTCGAC  GGTACCTTGG TTTTTAAAAC CAGCCTGGAG (SEQ ID NO 5)        SalI   KpnI 13.2 5′ CCTAGCGGCA ATGGCTACAG GTGAGTACTC GCGGGCTGGGCG (SEQ ID NO 6) 13.3 5′ CGCCCAGCCC GCGAGTACTC ACCTGTAGCC ATTGCCGCTA GG(SEQ ID NO 7) 13.4 5′ TTTTCTCGAG  CTAGAACAGA TAGCCAGGCT GAGAG (SEQ ID NO8)        XhoI

 The non-boldface region of oligo 13.1 is identical to the MMT-Ipromoter, with the natural KpnI site as its 5′ boundary. The boldfacetype denotes a SalI site tail to convert the 5′ boundary to a SalI site.The boldface region of oligos 13.2 and 13.3 denote hGH sequences, whilethe non-boldface regions are intron 1 sequences from the hEPO gene. Thenon-boldface region of oligo 13.4 is identical to last 25 bases of hEPOintron 1. The boldface region includes an XhoI site tail to convert the3′ boundary of the amplified fragment to an XhoI site.

Plasmid pXEPO-11 is designed to place, by gene targeting, the MMT-Ipromoter and exon 1 of hGH upstream of the hEPO structural gene andpromoter region at the endogenous hEPO locus on human chromosome 7.Plasmid pXEPO-11 is constructed as follows oligonucleotides 13.1 and13.5-13.7 are utilized in polymerase chain reactions to generate afusion fragment in which the mouse metallothionein I (mMT-I)promoter—hGH exon 1 sequences are additionally fused to hEPO sequencesfrom −1 to −630 relative to the hEPO coding region. First,oligonucleotides 13.1 and 13.5 are used to amplify the approximately0.73 kb mMT-I promoter—hGH exon 1 fragment from pXGH5 (FIG. 1). Next,oligonucleotides 13.6 and 13.7 are used to amplify, from human genomicDNA, the approximately 0.62 kb fragment comprised predominantly of hEPOsequences from −1 to −620 relative to the hEPO coding region. Botholigos 13.5 and 13.6 contain a 10 bp linker sequence located at the hGHintron 1—hEPO promoter region, which corresponds to the natural hEPOintron 1 splice donor site. Finally, the two amplified fragments aremixed and further amplified with oligonucleotides 13.1 and 13.7 togenerate the final fusion fragment (fusion fragment 6) flanked by a SalIsite at the 5′ side of the mMT-I moiety and an XhoI site at the 3′ sideof the hEPO promoter region. Fusion fragment 6 is digested with XhoI andSalI and ligated to XhoI digested pT163. The ligation mixture istransformed into E. coli and a clone containing a single insert offusion fragment 6 in which the XhoI site is regenerated at the 3′ sideof hEPO promoter sequences is identified and designated pXEPO-11.

13.5 5′ CCTAGCGGCA ATGGCTACAG GTGAGTACTC AAGCTTCTGG GCTTCCAGAC CCAG (SEQID NO 9)                                        HindIII 13.6 5′CTGGGTCTGG AAGCCCAGAA GCTT GAGTAC TCAC CTGTAG CCATTGCCGC TAGG (SEQ ID NO10)                        HindIII 13.7 5′ TTTTCTCGAG  CTCCGCGCCTGGCCGGGGTC CCTC (SEQ ID NO 11)         XhoI

 The boldface regions of oligos 13.5 and 13.6 denote hGH sequences. Theitalicized regions correspond to the first 10 base pairs of hEPOintron 1. The remainder of the oligos correspond to hEPO sequences from−620 to −597 relative to the hEPO coding region. The non-boldface regionof oligo 13.7 is identical to bases −1 to −24 relative to the hEPOcoding region. The boldface region includes an XhoI site tail to convertthe 3′ boundary of the amplified fragment to an XhoI site.

Plasmid pXEPO-10 can be used for gene targeting by digestion with BamHIand XhoI to release the 7.3 kb fragment containing the mMT-I/hGH fusionflanked on both sides by hEPO sequences. This fragment (targetingfragment 1) contains no hEPO coding sequences, having only sequenceslying between −620 and approximately '6620 upstream of the hEPO codingregion and hEPO intron 1 sequences to direct targeting to the human EPOlocus. targeting fragment 1 is transfected into primary or secondaryhuman skin fibroblasts using conditions similar to those described inExample 1c. G418-resistant colonies are picked into individual wells of96-well plates and screened for EPO expression by an ELISA assay (R&DSystems, Minneapolis Minn.). Cells in which the transfecting DNAintegrates randomly into the human genome cannot produce EPO. Cells inwhich the transfecting DNA has undergone homologous recombination withthe endogenous hEPO intron 1 and hEPO upstream sequences contain achimeric gene in which the MMT-I promoter and non-transcribed sequencesand the hGH 5′ untranslated sequences and hGH exon 1 replace the normalhEPO promoter and hEPO exon 1 (see FIG. 5). Non-hEPO sequences intargeting fragment 1 are joined to hEPO sequences down-stream of hEPOintron 1. The replacement of the normal hEPO regulatory region with themMT-I promoter will activate the EPO gene in fibroblasts, which do notnormally express EPO. The replacement of hEPO exon 1 with hGH exon 1results in a protein in which the first 4 amino acids of the hEPO signalpeptide are replaced with amino acids 1-3 of hGH, creating a functional,chimeric signal peptide which is removed by post-translation processingfrom the mature protein and is secreted from the expressing cells.

Plasmid pXEPO-11 can be used for gene targeting by digestion with BamHIand XhoI to release the 7.4 kb fragment containing the mMT-I/hGH fusionflanked on both sides by hEPO sequences. This fragment (targetingfragment 2) contains no hEPO coding sequences, having only sequenceslying between −1 and approximately −6620 upstream of the hEPO codingregion to direct targeting to the human EPO locus. Targeting fragment 2is transfected into primary or secondary human skin fibroblasts usingconditions similar to those described in Example 1 g. G418-resistantcolonies are picked into individual wells of 96-well plates and screenedfor EPO expression by an ELISA assay (R&D Systems, Minneapolis, Minn.).Cells in which the transfecting DNA integrates randomly into the humangenome cannot produce EPO. Cells in which the transfecting DNA hasundergone homologous recombination with the endogenous hEPO promoter andupstream sequences contain a chimeric gene in which the mMT-I promoterand non-transcribed sequences, hGH 5′ untranslated sequences and hGhexon 1, and a 10 base pair linker comprised of the first 10 bases ofhEPO intron 1 are inserted at the HindIII site lying at position −620relative to the hEPO coding region (see FIG. 6). The localization of themMT-I promoter upstream of the normally silent hEPO promoter will directthe synthesis, in primary or secondary skin fibroblasts, of a messagereading (5′ to 3′) non-translated metallothionein and hGH sequences, hGHexon 1, 10 bases of DNA identical to the first 10 base pairs of hEPOintron 1, and the normal hEPO promoter and hEPO exon 1 (−620 to +13relative to the EPO coding sequence). The 10 base pair linker sequencefrom hEPO intron 1 acts as a splice donor site to fuse hGH exon 1 to thenext downstream splice acceptor site, that lying immediately upstream ofhEPO exon 2. Processing of the resulting transcript will thereforesplice out the hEPO promoter, exon 1, and intron 1 sequences. Thereplacement of hEPO exon 1 with hGH exon 1 results in a protein in whichthe first 4 amino acids of the hEPO signal peptide are replaced withamino acids 1-3 of hGH, creating a functional, chimeric signal peptidewhich is removed by post-translation processing from the mature proteinand is secreted from the expressing cells.

A series of constructs related to pXEPO-10 and PXEPO-11 can beconstructed, using known methods. In these constructs, the relativepositions of the mMT-I promoter and hGH sequences, as well as theposition at which the mMT-I/hGH sequences are inserted into hEPOupstream sequences, are varied to create alternative chimerictranscription units that facilitate gene targeting, result in moreefficient expression of the fusion transcripts, or have other desirableproperties. Such constructs will give similar results, such that anhGH-hEPO fusion gene is placed under the control of an exogenouspromoter by gene targeting to the normal hEPO locus. For example, the 6kb HindIII-BamHI fragment upstream of the hEPO gene (See Example if) hasnumerous restriction enzyme recognition sequences that can be utilizedas sites for insertion of the neo gene and the mMT-I promoter/hGH fusionfragment. One such site, a BglII site lying approximately 1.3 kbupstream of the HindIII site, is unique in this region and can be usedfor insertion of one or more selectable markers and a regulatory regionderived from another gene that will serve to activate EPO expression inprimary, secondary, or immortalized human cells.

First, the intermediate plasmid pT164 is constructed by inserting the 6kb HindIII-BamHI fragment (Example 1f) lying upstream of the hEPO codingregion into HindIII-BamHI digested pBluescriptII SK+ (Stratagene,LaJola, Calif.). Plasmid pMC1neoPolyA (Thomas, K. R. and Capecchi, M. R.Cell 51:503-512 (1987); available from Stratagene, LaJola, Calif. isdigested with BamHI and XhoI, made blunt-ended by treatment with theKlenow fragment of E. coli DNA polymerase, and the resulting 1.1 kbfragment is purified. pT164 is digested with BglII and made blunt-endedby treatment with the Klenow fragment of E. coli DNA polymerase. The twopreceding blunt-ended fragments are ligated together and transformedinto competent E. coli. Clones with a single insert of the 1.1 kb neofragment are isolated and analyzed by restriction enzyme analysis toidentify those in which the BglII site recreated by the fusion of theblunt XhoI and BglII sites is localized 1.3 kb away from the uniqueHindIII site present in plasmid pT164. The resulting plasmid, pT165, cannow be cleaved at the unique BglII site flanking the 5′ side of the neotranscription unit.

Oligonucleotides 13.8 and 13.9 are utilized in polymerase chainreactions to generate a fragment in which the mouse metallothionein I(mMT-I) promoter—hGH exon 1 sequences are additionally fused to a 10base pair fragment comprising a splice donor site. The splice donor sitechosen corresponds to the natural hEPO intron 1 splice donor site,although a larger number of splice donor sites or consensus splice donorsites can be used. The oligonucleotides (13.8 and 13.9) are used toamplify the approximately 0.73 kb mMT-I promoter—hGH exon 1 fragmentfrom pXGH5 (FIG. 1). The amplified fragment (fragment 7) is digestedwith BglII and ligated to BglII digested pT165. The ligation mixture istransformed into E. coli and a clone, containing a single insert offragment 7 in which the KpnI site in the mMT-I promoter is adjacent tothe 5′ end of the neo gene and the mMT-I promoter is oriented such thattranscription is directed towards the unique HindIII site, is identifiedand designated pXEPO-12.

13.8 5′ AAAAAGATCT  GGTACCTTGG TTTTTAAAAC CAGCCTGGAG (SEQ ID NO 12)       BglII   KpnI

 The non-boldface region of oligo 13.8 is identical to the mMT-Ipromoter, with the natural KpnI site as its 5′ boundary. The boldfacetype denotes a BglII site tail to convert the 5′ boundary to a BglIIsite.

13.9 5′ TTTTAGATCT GAGTACTCAC CTGTAGCCAT TGCCGCTAGG (SEQ ID NO 13)        BglII

 The boldface region of oligos 13.9 denote hGH sequences. The italicizedregion corresponds to the first 10 base pairs of hEPO intron 1. Theunderlined BglII site is added for plasmid construction purposes.

Plasmid pXEPO-12 can be used for gene targeting by digestion with BamHIand HindIII to release the 7.9 kb fragment containing the neo gene andthe mMT-I/hGH fusion flanked on both sided by hEPO sequences. Thisfragment (targeting fragment 3) contains no hEPO coding sequences,having only sequences lying between approximately −620 and approximately−6620 upstream of the hEPO coding region to direct targeting upstream ofthe human EPO locus. Targeting fragment 3 is transfected into primary,secondary, or immortalized human skin fibroblasts using conditionssimilar to those described in Examples 1b and 1c. G418-resistantcolonies are picked into individual wells of 96-well plates and screenedfor EPO expression by an ELISA assay (R&D Systems, Minneapolis Minn).Cells in which the transfecting DNA integrates randomly into the humangenome cannot produce EPO. Cells in which the transfecting DNA hasundergone homologous recombination with the endogenous hEPO promoter andupstream sequences contain a chimeric gene in which the mMT-I promoterand non-transcribed sequences, hGH 5′ untranslated sequences, and hGHexon 1, and a 10 base pair linker comprised of the first 10 bases ofhEPO intron 1 are inserted at the BglII site lying at positionapproximately −1920 relative to the hEPO coding region. The localizationof the mMT-I promoter upstream of the normally silent hEPO promoter willdirect the synthesis, in primary, secondary, or immortalized humanfibroblasts (or other human cells), of a message reading: (5′ to 3′)nontranslated metallothio-nein and hGH sequences, hGH exon 1, 10 basesof DNA identical to the first 10 base pairs of hEPO intron 1, and hEPOupstream region and hEPO exon 1 (from approximately −1920 to +13relative to the EPO coding sequence). The 10 base pair linker sequencefrom hEPO intron 1 acts as a splice donor site to fuse hGH exon 1 to adownstream splice acceptor site, that lying immediately upstream of hEPOexon 2. Processing of the resulting transcript will therefore splice outthe hEPO upstream sequences, promoter region, exon 1, and intron 1sequences. When using pXEPO-10, −11 and −12, post-transcriptionalprocessing of the message can be improved by using in vitro mutagenesisto eliminate splice acceptor sites lying in hEPO upstream sequencesbetween the mMT-I promoter and hEPO exon 1, which reduce level ofproductive splicing events needed create the desired message. Thereplacement of hEPO exon 1 with hGH exon 1 results in a protein in whichthe first 4 amino acids of the hEPO signal peptide are replaced withamino acids 1-3 of hGH, creating a functional, chimeric signal peptidewhich is removed by post-translation processing from the mature proteinand is secreted from the expressing cells.

Example 3 Targeted Modification of Sequences Upstream and Amplificationof the Targeted Gene

Human cells in which the EPO gene has been activated by the methodspreviously described (in copending U.S. patent applications Ser. Nos.07/787,840 and 07/911,533) can be induced to amplify the neo/mMT-1 /EPOtranscription unit if the targeting plasmid contains a marker gene thatcan confer resistance to a high level of a cytotoxic agent by thephenomenon of gene amplification. Selectable marker genes such asdihydrofolate reductase (dhfr, selective agent is methotrexate), themultifunctional CAD gene [encoding carbamyl phosphate synthase,aspartate transcarbamylase, and dihydro-orotase; selective agent isN-(phosphonoacetyl)-L-aspartate (PALA)], and adenosine deaminase (ada;selective agent is an adenine nucleoside), have been documented, amongother genes, to be amplifiable in immortalized human cell lines (Wright,J. A. et al. Proc. Natl. Acad. Sci. USA 87:1791-1795 (1990)). In thesestudies, gene amplification has been documented to occur in a number ofimmortalized human cell lines. HT1080, HeLa, MCF-7 breast cancer cells,K-562 leukemia cells, KB carcinoma cells, or 2780AD ovarian carcinomacells all display amplification under appropriate selection conditions.

Plasmids pXEPO-10 and pXEPO-11 can be modified by the insertion of anormal or mutant dhfr gene into the unique HindIII sites of theseplasmids. After transfection of HT1080 cells with the appropriate DNA,selection for G418-resistance (conferred by the neo gene), andidentification of cells in which the hEPO gene has been activated bygene targeting of the neo, dhfr, and mMT-1 sequences to the correctposition upstream of the hEPO gene, these cells can be exposed tostepwise selection in methotrexate (MTX) in order to select foramplification of dhfr and co-amplification of the linked neo, mMT-1, andhEPO sequences (Kaufman, R. J. Technique 2:221-236 (1990)). A stepwiseselection scheme in which cells are first exposed to low levels of MTX(0.01 to 0.08 μM), followed by successive exposure to incrementalincreases in MTX concentrations up to 250 μM MTX or higher is employed.Linear incremental steps of 0.04 to 0.08 μM MTX and successive 2-foldincreases in MTX concentration will be effective in selecting foramplified transfected cell lines, although a variety of relativelyshallow increments will also be effective. Amplification is monitored byincreases in dhfr gene copy number and confirmed by measuring in vitrohEPO expression. By this strategy, substantial overexpression of hEPOcan be attained by targeted modification of sequences lying completelyoutside of the hEPO coding region.

Constructs similar to those described (Examples 1i and 1k) to activatehGH expression in human cells can also be further modified to includethe dhfr gene for the purpose of obtaining cells that overexpress thehGH gene by gene targeting to non-coding sequences and subsequentamplification.

Example 4 Targeting and Activation of the Human EPO Locus in anImmortalized Human Fibroblast Line

The targeting construct pXEPO-13 was made to test the hypothesis thatthe endogenous hEPO gene could be activated in a human fibroblast cell.First, plasmid pT22.1 was constructed, containing 63 bp of genomic hEPOsequence upstream of the first codon of the hEPO gene fused to the mousemetallothionein-1 promoter (mMT-I). Oligonucleotides 22.1 to 22.4 wereused in PCR to fuse mMT-I and hEPO sequences. The properties of theseprimers are as follows: 22.1 is a 21 base oligonucleotide homologous toa segment of the mMT-I promoter beginning 28 bp upstream of the mMT-IKpnI site; 22.2 and 22.3 are 58 nucleotide complementary primers whichdefine the fusion of hEPO and mMT-I sequences such that the fusioncontains 28 bp of hEPO sequence beginning 35 bases upstream of the firstcodon of the hEPO gene, and mMT-I sequences beginning at base 29 ofoligonucleotide 22.2, comprising the natural BglII site of mMT-I andextending 30 bases into mMT-I sequence; 22.4 is 21 nucleotides in lengthand is homologous to hEPO sequences beginning 725 bp downstream of thefirst codon of the hEPO gene. These primers were used to amplify a 1.4kb DNA fragment comprising a fusion of mMT-I and hEPO sequences asdescribed above. The resulting fragment was digested with KpnI (the PCRfragment contained two KpnI sites: a single natural KpnI site in themMT-I promoter region and a single natural KpnI site in the hEPOsequence), and purified. The plasmid pXEPO1 (FIG. 3) was also digestedwith KpnI, releasing a 1.4 kb fragment and a 6.4 kb fragment. The 6.4 kbfragment was purified and ligated to the 1.4 kb KpnI PCR fusionfragment. The resulting construct was called pT22.1. A secondintermediate, pT22.2, was constructed by ligating the approximately 6 kbHindIII-BamHI fragment lying upstream of the hEPO structural gene (seeExample 1f) to BamHI and HindIII digested pBSIISK+ (Stratagene, LaJola,Calif.). A third intermediate, pT22.3, was constructed by first excisinga 1.1 kb XhoI/BamHI fragment from pMCINEOpolyA (Stratagene., LaJola,Calif.) containing the neomycin phosphotransferase gene. The fragmentwas then made blunt-ended with the Klenow fragment of DNA polymerase I(New England Biolabs). This fragment was then ligated to the HincII siteof pBSIISK+ (similarly made blunt with DNA polymerase I) to producepT22.3. A fourth intermediate, pT22.4, was made by purifying a 1.1 kbXhoI/HindIII fragment comprising the neo gene from pT22.3 and ligatingthis fragment to XhoI and HindIII digested pT22.2. pT22.4 thus containsthe neo gene adjacent to the HindIII side of the BamHI-HindIII upstreamhEPO fragment. Finally, pXEPO-13 was generated by first excising a 2.0kb EcoRI/AccI fragment from pT22.1. The EcoRI site of this fragmentdefines the 5′ boundary of the mMT-I promoter, while the AccI site ofthis fragment lies within hEPO exon 5. Thus, the AccI/EcoRI fragmentcontains a nearly complete hEPO expression unit, missing only a part ofexon 5 and the natural polyadenylation site. This 2.0 kb EcoRI/AccIfragment was purified, made blunt-ended by treatment with the Klenowfragment of DNA polymerase I, and ligated to XhoI digested, blunt-ended,pT22.4.

HT1080 cells were transfected with PvuI-BamHI digested pXEPO-13.pXEPO-13 digested in this way generates three fragments; a 1 kb vectorfragment including a portion of the amp gene, a 1.7 kb fragment ofremaining vector sequences and an approximately 10 kb fragmentcontaining hEPO, neo and mMT-I sequences. This approximately 10 kbBamHI/PvuI fragment contained the following sequences in order from theBamHI site: an approximately 6.0 kb of upstream hEPO genomic sequence,the 1.1 kb neo transcription unit, the 0.7 kb mMT-I promoter and the 2.0kb fragment containing hEPO coding sequence truncated within exon 5.45μg of pEXPO-13 digested in this way was used in an electroporation of12 million cells (electroporation conditions were described in Example1b). This electroporation was repeated a total of eight times, resultingin electroporation of a total of 96 million cells. Cells were mixed withmedia to provide a cell density of 1 million cells per ml and 1 mlaliquots were dispensed into a total of 96, 150 mm tissue culture plates(Falcon) each containing a minimum of 35 ml of DMEM/15% calf serum. Thefollowing day, the media was aspirated and replaced with fresh mediumcontaining 0.8 mg/ml G418 (Gibco). After 10 days of incubation, themedia of each plate was sampled for hEPO by ELISA analysis (R & DSystems). Six of the 96 plates contained at least 10 mU/ml hEPO. One ofthese plates, number 18, was selected for purification of hEPOexpressing colonies. each of the 96, 150 mm plates containedapproximately 600 G418 resistant colonies (an estimated total of 57,600G418 resistant colonies on all 96 plates). The approximately 600colonies on plate number 18 were trypsinized and replated at 50 cells/mlinto 364 well plates (Sterilin). After one week of incubation, singlecolonies were visible at approximately 10 colonies per large well of the364 well plates (these plates are comprised of 16 small wells withineach of the 24 large wells). Each well was screened for hEPO expressionat this time. Two of the large wells contained media with at least 20mU/ml hEPO. Well number A2 was found to contain 15 colonies distributedamong the 16 small wells. The contents of each of these small wells weretrypsinized and transferred to 16 individual wells of a 96 well platefollowing 7 days of incubation the media from each of these wells wassampled for hEPO ELISA analysis. Only a single well, well number 10,contained hEPO. This cell strain was designated HT165-18A2-10 and wasexpanded in culture for quantitative hEPO analysis, RNA isolation andDNA isolation. Quantitative measurement of hEPO production resulted in avalue of 2,500 milliunits/million cells/24 hours.

A 0.2 kb DNA probe extending from the AccI site in hEPO exon 5 to theBglII site in the 3′ untranslated region was used to probe RNA isolatedfrom HT165-18A2-10 cells. The targeting construct, pXEPO-13, truncatedat the AccI site in exon 5 does not contain these AccI/BglII sequencesand, therefore, is diagnostic for targeting at the hEPO locus. Only cellstrains that have recombined in a homologous manner with natural hEPOsequences would produce an hEPO mRNA containing sequence homologous tothe AccI/BglII sequences. HT165-18A2-10 was found to express an mRNA ofthe predicted size hybridizing with the 32-P labeled AccI/BglII hEPOprobe on Northern blots. Restriction enzyme and Southern blot analysisconfirmed that the neo gene and mMT-I promoter were targeted to one ofthe two hEPO alleles in HT165-18A2-10 cells.

These results demonstrate that homologous recombination can be used totarget a regulatory region to a gene that is normally silent in humanfibroblasts, resulting in the functional activation of that gene.

22.1 5′ CACCTAAAAT GATCTCTCTG G (SEQ ID NO 14) 22.2 5′ CGCGCCGGGTGACCACACCG GGGGCCCTAG ATCTGGTGAA GCTGGAGCTA CGGAGTAA (SEQ ID NO 15) 22.35′ TTACTCCGTA GCTCCAGCTT CACCAGATCT AGGGCCCCCG GTGTGGTCAC CCGGCGCG (SEQID NO 16) 22.4 5′ GTCTCACCGT GATATTCTCG G (SEQ ID NO 17)

EXAMPLE 5 Production of Intronless Genes

Gene targeting can also be used to produce a processed gene, devoid ofintrons, for transfer into yeast or bacteria for gene expression and invitro protein production. For example, hGH can by produced in yeast bythe approach described below.

Two separate targeting constructs are generated. Targeting construct 1(TC1) includes a retroviral LTR sequence, for example the LTR from theMoloney Murine Leukemia Virus (MoMLV), a marker for selection in humancells (e.g., the neo gene from Tn5), a marker for selection in yeast(e.g., the yeast URA3 gene), a regulatory region capable of directinggene expression in yeast (e.g., the GAL4 promoter), and optionally, asequence that, when fused to the hGH gene, will allow secretion of hGHfrom yeast cells (leader sequence). The vector can also include a DNAsequence that permits retroviral packaging in human cells. The constructis organized such that the above sequences are flanked, on both sides,by hGH genomic sequences which, upon homologous recombination withgenomic hGH gene N sequences, will integrate the exogenous sequences inTC1 immediately upstream of hGH gene N codon 1 (corresponding to aminoacid position 1 in the mature, processed protein). The order of DNAsequences upon integration is: hGH upstream and regulatory sequences,neo gene, LTR, URA3 gene, GAL4 promoter, yeast leader sequence, hGHsequences including and downstream of amino acid 1 of the matureprotein. Targeting Construct 2 (TC2) includes sequences sufficient forplasmid replication in yeast (e.g., 2-micron circle or ARS sequences), ayeast transcriptional termination sequence, a viral LTR, and a markergene for selection in human cells (e.g., the bacterial gpt gene). Theconstruct is organized such that the above sequences are flanked on bothsides by hGH genomic sequences which, upon homologous recombination withgenomic hGH gene N sequences, will integrate the exogenous sequences inTC2 immediately downstream of the hGH gene N stop codon. The order ofDNA sequences upon integration is: hGH exon 5 sequences, yeasttranscription termination sequences, yeast plasmid replicationsequences, LTR, gpt gene, hGH 3′ non-translated sequences.

Linear fragments derived from TC1 and TC2 are sequentially targeted totheir respective positions flanking the hGH gene. After superinfectionof these cells with helper retrovirus, LTR directed transcriptionthrough this region will result in an RNA with LTR sequences on bothends. Splicing of this RNA will generate a molecule in which the normalhGH introns are removed. Reverse transcription of the processedtranscript will result in the accumulation of double-stranded DNA copiesof the processed hGH fusion gene. DNA is isolated from thedoubly-targeted, retrovirally-infected cells, and digested with anenzyme that cleaves the transcription unit once within the LTR. Thedigested material is ligated under conditions that promotecircularization, introduced into yeast cells, and the cells aresubsequently exposed to selection for the URA3 gene only cells whichhave taken up the URA3 gene (linked to the sequences introduced by TC1and TC2 and the processed hGH gene) can grow. These cells contain aplasmid which will express the hGH protein upon galactose induction andsecrete the hGH protein from cells by virtue of the fused yeast leaderpeptide sequence which is cleaved away upon secretion to produce themature, biologically active, hGH molecule.

Expression in bacterial cells is accomplished by simply replacing, inTC1 and TC2, the ampicillin-resistance gene from pBR322 for the yeastURA3 gene, the tac promoter (deBoer et al., Proc. Natl. Acad. Sci.80:21-25 (1983)) for the yeast GAL4 promoter, a bacterial leadersequence for the yeast leader sequence, the pBR322 origin of replicationfor the 2-micron circle or ARS sequence, and a bacterial transcriptionaltermination (e.g., trpA transcription terminator; Christie, G. E. etal., Proc. Natl. Acad. Sci, 78:4180-4184 (1981)) sequence for the yeasttranscriptional termination sequence. Similarly, hEPO can be expressedin yeast and bacteria by simple replacing the hGH targeting sequenceswith hEPO targeting sequences, such that the yeast or bacterial leadersequence is positioned immediately upstream of hEPO codon 1(corresponding to amino acid position 1 in the mature processedprotein).

Equivalents

Those skilled in the art will recognize, or be able to ascertain usingnot more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

17 19 base pairs nucleic acid single linear DNA (genomic) 1 AGCTTCTGGGCTTCCAGAC 19 16 base pairs nucleic acid single linear DNA (genomic) 2GGGGTCCCTC AGCGAC 16 17 base pairs nucleic acid single linear DNA(genomic) 3 TGGGCTTCCA GACCCAG 17 20 base pairs nucleic acid singlelinear DNA (genomic) 4 CCAGCTACTT TGCGGAACTC 20 40 base pairs nucleicacid single linear DNA (genomic) 5 AAAAGTCGAC GGTACCTTGG TTTTTAAAACCAGCCTGGAG 40 42 base pairs nucleic acid single linear DNA (genomic) 6CCTAGCGGCA ATGGCTACAG GTGAGTACTC GCGGGCTGGG CG 42 42 base pairs nucleicacid single linear DNA (genomic) 7 CGCCCAGCCC GCGAGTACTC ACCTGTAGCCATTGCCGCTA GG 42 35 base pairs nucleic acid single linear DNA (genomic)8 TTTTCTCGAG CTAGAACAGA TAGCCAGGCT GAGAG 35 54 base pairs nucleic acidsingle linear DNA (genomic) 9 CCTAGCGGCA ATGGCTACAG GTGAGTACTCAAGCTTCTGG GCTTCCAGAC CCAG 54 54 base pairs nucleic acid single linearDNA (genomic) 10 CTGGGTCTGG AAGCCCAGAA GCTTGAGTAC TCACCTGTAG CCATTGCCGCTAGG 54 34 base pairs nucleic acid single linear DNA (genomic) 11TTTTCTCGAG CTCCGCGCCT GGCCGGGGTC CCTC 34 40 base pairs nucleic acidsingle linear DNA (genomic) 12 AAAAAGATCT GGTACCTTGG TTTTTAAAACCAGCCTGGAG 40 31 base pairs nucleic acid single linear DNA (genomic) 13TTTTGTCGAC GGTACCTTGG TTTTTAAAAC C 31 21 base pairs nucleic acid singlelinear DNA (genomic) 14 CACCTAAAAT GATCTCTCTG G 21 58 base pairs nucleicacid single linear DNA (genomic) 15 CGCGCCGGGT GACCACACCG GGGGCCCTAGATCTGGTGAA GCTGGAGCTA CGGAGTAA 58 58 base pairs nucleic acid singlelinear DNA (genomic) 16 TTACTCCGTA GCTCCAGCTT CACCAGATCT AGGGCCCCCGGTGTGGTCAC CCGGCGCG 58 21 base pairs nucleic acid single linear DNA(genomic) 17 GTCTCACCGT GATATTCTCG G 21

What is claimed is:
 1. A method of altering the expression of a targetedgene in a cell, the method comprising the steps of: (a) providing a DNAconstruct comprising: (i) a targeting sequence; (ii) an exogenousregulatory sequence; (iii) an exon; and (iv) an unpaired splice-donorsite at the 3′ end of the exon, (b) providing a cell, the genome ofwhich comprises (i) a target site homologous to the targeting sequence,and; (ii) a targeted gene having an endogenous regulatory region; c)transfecting the cell with the DNA construct in vitro, thereby producinga transfected cell; d) maintaining the transfected cell under conditionsappropriate for homologous recombination, thereby producing ahomologously recombinant cell, the genome of which comprises theexogenous regulatory sequence, the construct-derived exon, and theconstruct-derived splice-donor site, in addition to all endogenous exonsof the targeted gene; and e) maintaining the homologously recombinantcell under conditions appropriate for transcription under the control ofthe exogenous regulatory sequence, to produce a transcript of theconstruct-derived exon, the targeted gene, and any sequence lyingbetween the construct-derived exon and the targeted gene, wherein theRNA of the transcript corresponding to the construct-derivedsplice-donor site directs splicing to a splice-acceptor site in thetranscript which corresponds to a site within the targeted gene.
 2. Themethod of claim 1 further comprising the steps of: (f) maintaining thehomologously recombinant cell under conditions appropriate for splicingand translation of the transcript; and (g) confirming that a translationproduct of the spliced transcript was produced.
 3. A cultured vertebratecell into the genome of which is incorporated transcription unit,wherein the transcription unit comprises an exogenous regulatorysequence, an exogenous exon, and a splice-donor site at the 3′ end ofthe exogenous exon, all located upstream of the endogenous transcriptioninitiation site of an endogenous gene, the splice-donor site beingoperatively linked to the endogenous splice-acceptor site of the secondendogenous exon of the endogenous gene.
 4. The cultured vertebrate cellof claim 3, wherein the cell is selected from the group consisting of:HT1080 cells, HeLa cells, MCF-7 breast cancer cells, K-562 leukemiacells, KB carcinoma cells, 2780AD ovarian carcinoma cells, chinesehamster ovary (CHO) cells, and mouse L cells.
 5. A cultured cell havingincorporated therein a new transcription unit, wherein the newtranscription unit comprises an exogenous inducible promoter operativelylinked to an endogenous gene in the chromosomal DNA of the cell,provided that the exogenous inducible promoter is not identical to theendogenous promoter of the endogenous gene, and wherein the cell isselected from the group consisting of HT1080 cells, MCF-7 breast cancercells, K-562 leukemia cells, KB carcinoma cells, 2780AD ovariancarcinoma cells, Chinese hamster ovary (CHO) cells, and mouse L cells.6. A method of providing a protein to a mammal, comprising introducinginto the mammal a homologoudsly recombinant cell which produces theprotein, the homologously recombinant cell being generated by an invitro process comprising: (a) providing a DNA construct comprising: (1)a targeting sequence, (2) an exogenous regulatory sequence, (3) an exon,and (4) an unpaired splice-donor site at the 3′ end of the exon (b)providing a vertebrate cell, the genome of which comprises; (i) a targetsite homologous to the targeting sequence, and (ii) a targetedendogenous gene having an endogenous regulatory region; (c) transfectingthe vertebrate cell with the DNA construct, thereby producing atransfected cell; (d) maintaining the transfected cell under conditionsappropriate for homologous recombination, thereby producing ahomologously recombinant cell the genome of which comprises theexogenous regulatory sequence, the construct-derived exon, and theconstruct-derived splice-donor site, in addition to all endogenous exonsof the targeted gene; and (e) maintaining the homologously recombinantcell under conditions appropriate for transcription under the control ofthe exogenous regulatory sequence, to produce a transcript of theconstruct-derived exon, the targeted gene, and any sequence lyingbetween the construct-derived exon and the targeted gene, wherein theRNA of the transcript corresponding to the construct-derivedsplice-donor site directs splicing to a splice-acceptor site in thetranscript which corresponds to a site within the targeted gene.
 7. Themethod of claim 6, wherein the homologously recombinant cell is, priorto introduction into the mammal, enclosed within a barrier device whichpermits passage of the protein from the interior of the barrier deviceto the exterior of the barrier device.
 8. A DNA construct that altersthe expression of a targeted gene in a cell when the DNA construct ishomologously recombined with a target site within the chromosomal DNA ofthe cell, the DNA construct comprising: (a) a targeting sequencehomologous to the target site; (b) an exogenous regulatory sequence; (c)an exon; and (d) an unpaired splice-donor site at the 3′ end of theexon; wherein, following homologous recombination of the targetingsequence with the target site, the chromosomal DNA of the cell comprisesthe construct-derived exon in addition to all endogenous exons of thetargeted gene, and wherein the targeted gene encodes a hormone, acytokine, an antigen, an antibody, an enzyme, a clotting factor, atransport protein, a receptor, a regulatory protein, a structuralprotein, or a transcription factor.
 9. A DNA construct that alters theexpression of a targeted gene in a cell when the DNA construct ishomologously recombined with a target site within the chromosomal DNA ofthe cell, the DNA construct comprising: (a) a targeting sequencehomologous to the target site; (b) an exogenous regulatory sequence; (c)an exon; and (d) an unpaired splice-donor site at the 3′ end of theexon; wherein, following homologous recombination of the targetingsequence with the target site, the chromosomal DNA of the cell comprisesthe construct-derived exon in addition to all endogenous exons of thetargeted gene, and wherein the targeted gene encodes a protein selectedfrom the group consisting of calcitonin, insulin, insulinotropin,insulin-like growth factors, parathyroid hormone, nerve growth factors,interleukins, immunoglobulins, catalytic antibodies, superoxidedismutase, tissue plasminogen activators, blood clotting factor VIII,apolipoprotein E, apolipoprotein A-I, globins, low density lipoproteinreceptor, IL2 receptor, IL-2 receptor antagonists, alpha-1 antitrypsin,immune response modifiers, growth hormone, interferon, blood clottingfactor IX, glucocerebrosidase, a colony stimulating factor, anderythropoietuin..
 10. A DNA construct that alters the expression of atargeted gene in a cell when the DNA construct is homologouslyrecombined with a target site within the chromosomal DNA of the cell,the DNA construct comprising: (a) a targeting sequence homologous to thetarget site; (b) an exogenous regulatory sequence; (c) an exon; and (d)an unpaired splice-donor site at the 3′ end of the exon; wherein,following homologous recombination of the targeting sequence with thetarget site, the chromosomal DNA of the cell comprises theconstruct-derived exon in addition to all endogenous exons of thetargeted gene, and wherein the exogenous regulatory sequence is apromoter, an enhancer, a scaffold-attachment region, a negativeregulatory element, a transcriptional initiation site, or a regulatoryprotein binding site.
 11. A DNA construct that alters the expression ofa targeted gene in a cell when the DNA construct is homologouslyrecombined with a target site within the chromosomal DNA of the cell,the DNA construct comprising: (a) a targeting sequence homologous to thetarget site; (b) an exogenous regulatory sequence; (c) an exon; (d) anunpaired splice-donor site at the 3′ end of the exon; and (e) anamplifiable marker gene; wherein, following homologous recombination ofthe targeting sequence with the target site, the chromosomal DNA of thecell comprises the construct-derived exon in addition to all endogenousexons of the targeted gene.